EMBO/sd-character-level-ner huggingface dataset:
I RIP-qPCR analysis of the interaction of TRAF4 with FLAG in cells overexpressing FLAG-YTHDF1. Enrichment of TRAF4 with FLAG was measured by qPCR and normalized to input.
Representative confocal microscope image of L6 cells stably expressing tandem fluorescent-eGFP-mCherry LC3B treated with iron (FeSO4, 250 µM) for the indicated time points (4 h, 8 h, 24 h). Quantification of mean LC3B puncta per cell from (A). Experiments were repeated three times, and one representative experiment is presented here.
Increased overall number of coated structures in stimulated endophilin 1/2-DKOs. (F') Both, coated vesicles and coated pits forming at ELVs were significantly increased in 1/2-DKO after stimulation. Mann-Whitney test; **p < 0.01; ***p < 0.001.
(D) Grk5 expression in NRCMs upon Cand2 KD and Cul1 neddylation inhibition (MLN) analysed by immunoblot and RT-qPCR. Analyzed by One-way ANOVA, n=4-5 biological replicates. Data information: Error bars indicate means ± SEM; * - P ≤ 0.05, ** - P ≤ 0.01, *** - P ≤ 0.001, **** - P ≤ 0.0001
A Histogram of the isotope ratio distribution before (left) and after (right) normalization and centering. The x‐axis shows the mitosis/interphase ratio on a log2 scale. Note that more cell surface proteins were recovered from the interphase cells prior to normalization.
(E) HeLa cells were transfected with control plasmid (pMKO) or pMKO-BimshRNA. Blots were probed with the indicated antibodies. Data are shown as mean ± SD. ∗∗∗p < 0.001.
B atg34Δ yeast cells containing HTB‐Atg34 were grown to mid‐log phase and treated with rapamycin. Atg34 was affinity purified and subjected to mass spectrometric phosphorylation mapping. Phosphorylation sites: enlarged; Atg11 binding region: green; lysine substitution: gray.
A AP was induced by 5 injections (IP) of cerulein at a dosage of 50 μg/kg. SAP was induced by AP and one injection of lipopolysaccharide (LPS, IP) at a dosage of 20 mg/kg. AP+ANGPTL4 (2 mg/kg) was induced by AP and one injection of ANGPTL4 (IP) at a dosage of 2 mg/kg. ANGPTL4 (4 mg/kg) was induced by two injections of ANGPTL4 (IP) at a dosage of 2 mg/kg. Mice were sacrificed 6 h after pancreatitis induction. (H&E and immunofluorescent staining for IL-1β (red) and amylase (green) was performed along with immunohistochemistry for ANGPTL4 in pancreas tissues (n = 10, each group). Scale bar represents 50 µm
F Representative reconstructions of RFP-birthdated control and β-catex3 iDCX neurons in 24-week old mice at 13dpT. Scale bar= 20µm.
C. Representative images of two-photon live imaging of the same glioma area of the same mouse on 2 and 5 weeks growth glioma (BFP positive) implanted in ROSAmT/mG::Pdgfb-iCre mouse (350µm depth stack). Note differences in network complexity and vessel diameter.
(A) Noise decomposition of model M4, estimated with 100 simulations of the data set using the posterior mean parameter values combined with the measured cell areas. The variable η2 represents the variance/mean2.
(A, B) SARS-CoV-2 binding to monocyte-derived DCs (A) or primary LCs (B) in absence or presence of UF heparin (250 IU/mL) or LMWH enoxaparin (250 IU/mL). Data information: Data show the mean values and error bars are the SEM. ordinary one-way ANOVA with Tukey's multiple-comparison test. *P≤0.05, **P≤0.01, ***P≤0.001, ****P≤0.0001 (A) (n=4), (B) (n=4) DCs: Dendritic cells, LCs: Langerhans cells,
JQ1 treatment inhibits retinal microglial activation in the rd10 retina. Intravitreal injection of JQ1 (or vehicle) was performed at PN14, as described in Fig. 1. Eyeballs were collected at PN18, PN24, and PN30. Cryosections were used for immunostaining and fluorescence microscopy. a-c Representative immunostaining images of microglial markers. Scale bar 50 μm. Blue DAPI staining of nuclei. d Quantification: IBA1, CD68, or TSPO positive cells per 500 μm ONL length; mean ± SEM, n = 6 mice. Quantification of IBA1 staining at all five time points (PN18-PN30) is presented in Additional file 1: Figure S3
C) TIFA-GFP oligomerization after 30 min of infection with selected mutants of the LPS biosynthesis pathway (MOI 10)
(d, e) GFP cleavage of Rpl25p-GFP was analysed in wild-type, ubp3Δ, atg9Δ and bre5Δ strains containing the indicated plasmids, and quantified at the times indicated as described in Fig. 1d. One of three representative experiments is shown for d. The average of three independent experiments is shown in e, and the statistical analysis showed that the standard deviation was less than 13% (Supplementary Information, Table S3).
Kaplan-Meier survival curves for patients carrying one or two MICA-129Met alleles (n = 214) stratified by treatment with ATG.
(L) Elevated KLF4 expression increases resistance to Olaparib in MDA-MB-468 (BRCA-proficient) cells, while disruption of KLF4 PARylation attenuates KLF4-driven resistance to Olaparib.
(F) CD86 and CD40 expression on WT (blue dots) and Irf3‑/‑Irf7‑/‑ (orange dots) BMDCs expressed as a fold change in the proportion of CD86+ CD40+ cells over unstimulated controls. Data are pooled from 2 independent experiments.
K Sniffing time in each trial of the five-trial social memory test. Mock (n=11) trial 5 vs. trial 6; ZIKV (n=16) trial 5 vs. trial 6. L Normalized sniffing time in each trial of the five-trial social memory test. Mock (n=11) trial 5 vs. trial 6; ZIKV (n=16) trial 5 vs. trial 6.
c, d, Kaplan-Meier analysis comparing overall survival (c) or PDAC-free survival (d) of Atg7+/+ (blue) or Atg7−/− (red) KrasG12D/+ mice.
(k) Diffusion map of pericytes colored by cell type and inferred pseudotime represents pericyte differentiation.
(F) Total yeast cell lysate, post mitochondrial supernatant, and HistodenzTM-purified mitochondria from the indicated strain (wild type, msp1Δ, pex19Δ, pex19Δmsp1Δ, pex3Δ, and pex3Δmsp1Δ) expressing Pex13-V5 (under its endogenous promotor) were separated by SDS-PAGE and immunoblotted for Pex13 (α-V5), cytochrome c (α-cyt c), and HSP70 (α-hsp70). (G) Total yeast cell lysate, post mitochondrial supernatant, and HistodenzTM-purified mitochondria from the indicated strain (wild type, msp1Δ, pex19Δ, pex19Δmsp1Δ, pex3Δ, and pex3Δmsp1Δ) expressing Pex11-V5 (under its endogenous promotor) were separated by SDS-PAGE and immunoblotted for Pex11 (α-V5) and porin (α-porin), cytochrome c (α-cyt c), and HSP70 (α-hsp70).
B qRT-PCR analysis of several TGF-β-related genes in pRH6 and 2a2iL-RH6. **P<0.01, ***P<0.001 (t-test). Data presented as mean ± SD (n=3).
G Activity of PBMCs challenged with ORNs and total S. aureus (Sa) RNA (Myd88d/d, mutant MyD88 expression not impairing LPS driven IL-8 production; n = 2).
MCF10A cells were pretreated for 15 minutes with either DMSO or 10uM BIRB, followed by 60 minutes with either DMSO, 25uM 4HNE, 5uM RSL3, 4HNE and BIRB or RSL3 and BIRB. mRNA was isolated and PROM2 expression was quantified by qPCR. Shown are three independent experiments with standard deviation (n=3 experiments per group). P‑values were obtained by unpaired Student's t‑test with *P<0.05, **p<0.01, ***p<0.005. Exact p‑values are reported in the Appendix Table S1.
(H) Left: Time course of normalized EGFP signal, as assessed by TIRF microscopy, from GRAMD1 TKO HeLa cells expressing either wild-type (WT) or mutant versions of EGFP-GRAM1b constructs as indicated. SMase treatment (100 mU/ml) is indicated. Right: Values of ΔF/F0 corresponding to the end of the experiment as indicated by the arrow [mean ± SEM, n = 126 cells (WT), n = 38 cells (K161A), n = 33 cells (R191A), n = 43 cells (K161A/R191A), n = 46 cells (R189W), n = 44 cells (R189W/R191A); data are pooled from six independent experiments for WT and two independent experiments for the rest; Dunnett's multiple comparisons test, **P = 0.0002 (WT vs. K161A) and **P < 0.0001 for the rest].
(C). Protein expression of KRAS. Protein expression was evaluated by Western blotting. Protein was isolated from HEK-293FT cells transfected with GFP, TruB1, mt1, or mt2 (overexpression, left), and TruB1 KD or ctrl (siRNA, right).
(E) HeLa cells were infected with 5 p.f.u. per cell of either Ad HA‐tBID or Ad LacZ for 7 h, the media being changed to EBSS for the last 3 h where indicated. Alternatively, cells were treated with 50 μM camptothecin for 3 h.
D. Northern blot analysis of V. cholerae wild-type strain examined for the expression of VcdRP monitored over bacterial growth in the indicated media. The solid triangle represents the band corresponding to the full length primary vcdRP transcript, whereas the open triangles correspond to the different processed isoforms. Probing with 5S rRNA confirmed equal loading.
(B) Relative transcript expression of Fibronectin, (C) Collagen I and (D) Collagen III to GAPDH.
D. Tumor volume quantification in response to anti-CSF1 or control antibodies (n=6 mice per group). Statistical analysis: D. Mann-Whitney u-test. Error bars: D: median interquartile.
(G) P-Taf12 was followed by anti-FLAG IB of protein extracts from WT and tor2-ts10 strains, grown in rich conditions at 25°C or shifted to 30°C for 4 and 6 hours. (F,G) Anti-tubulin IBs are shown as a control for loading between samples. Shown are IBs that are representative of 3 independent experiments. The star (*) symbol labels unspecific bands detected by the anti-FLAG or anti-CBP antibodies in S. pombe.
(C) Northern (top panel) and western (middle, bottom panels) blot analyses of total RNA and protein from SOD1G85R strains, with (M1/M1) or without (+/+) suppressor mutations, demonstrating that the levels of SOD1G85R mRNA and total protein are not changed by the suppressor mutation (M1/M1). The western blot lanes are from the same gel and exposure.
(A) bta-miR-10b and ssc-miR-205 miRNAs efficiently repress microinjected NanoLuc luciferase reporters carrying a perfectly complementary (1x perfect) miRNA binding site or four partially complementary (bulged) miRNA binding sites. Error bars = SD. Each data point represents a value obtained from five microinjected oocytes. Data were collected in two microinjection sessions, each microinjection session used a new batch of in vitro transcribed reporter mRNAs. Data information: asterisks indicate statistical significance (p-value) of one-tailed t-test, (*p < 0.05, **p < 0.01, ***p < 0.001).
First, we generated databases of all the putative ORFs encoded by the genomes of 109 different bacteria. The database of M. pneumoniae was used to perform the shotgun MS and RNA-Seq studies that were aimed at evaluating the coverage and performance of experimental approaches in the discovery of SEPs. In a parallel, experiment-independent manner, RanSEPs performed in silico predictions of potential novel proteins in the database. Results coming from both experimental and computational approaches are integrated in a validation step using a set of 570 SEPs characterized both in this work and in previous studies. Finally, RanSEPs predictions for the 109 bacterial genomes are combined together to assess the functional diversity and importance of predicted SEPs. The second part of the figure highlights how RanSEPs functions. In step 0 (grey box), RanSEPs detects annotated standard proteins (purple) and SEPs (yellow). By BlastP, non-conserved standard and SEP proteins are detected (pink and light pink, respectively). In parallel, protein features are computed and filtered by Recursive Feature Elimination. These features are combined with general features of biological interest. In step 1 (yellow box), RanSEPs randomly subsets annotated standard and small proteins into a positive (green and yellow), a feature (blue and yellow) and a negative (pink and light pink) set from the bulk of non-conserved sequences. During step 2 (blue box), specific features that vary with each iteration are appended. In step 3 (purple box), the labelled positive and negative sets are divided into training and test sets. Step 4 (green box) consists of collecting the classifiers and classification task results, and computing the final statistics and scores for all the sequences. Step 0 is only run once and then it is out of the iteration process. Steps 1 to 3 are repeated as many times as iterations selected by the user. Step 4 is computed at the end to integrate the results of each iteration.
Purified Drosophila Delta and Serrate NE3 proteins bind to liposomes (D) Binding is reduced in Delta∆β1-2, but not to the Serrate equivalent using liposomes composed of PC:PS:PE-fluoroscein (80:15:5). Notch binding to Drosophila Delta NE3 (E) WT and ∆β1-2 (Delta∆β1-2) variants both bind to Notch, unlike variant with F204A substitution in DSL domain. Comparisons were performed with a two-tailed unpaired t-test. Values are shown as scattered data points with the dark lines representing the means. ns, no significant difference, **P < 0.01; ***P < 0.0001.
(D, E) Quantification of areas innervated by ophthalmic branches of trigeminal ganglion and spinal nerve, normalized to WT littermates (each dot depicts one embryo). Area of ophthalmic branch in crmp2-/- was increased by 66% (p<0.05, n=10, 3 litters). For spinal nerves, total area in knockouts was increased by 45% (p<0.05, WT n=8, crmp2-/- n=7, 3 litters). Mean ± SD, * p<0.05, t-test.
(A) ELISA showing the dose-dependent binding of plate-bound MRC-1 peptides P2, P3, and the control peptides CP1 and CP2 to PLY (0-0.5 μM). BSA was used as negative control to show the binding specificity. Data are mean ± s.e.m. of two independent experiments, each containing three replicates per condition.
A. The discriminant microbial taxa of the ileum, cecum, and colon of ten adult CtM Hanwoo are shown, determined to the genus level by the linear discriminant analysis (LDA) effect size (LEfSe) method. The LDA scores represent the degree of consistent difference in the relative abundance between groups. For orphan sequences (i.e., unassigned at the genus level), a high-rank lineage is provided (f, family; o, order).
(F) GST-ALIX (lane 3), but not GST (lane 2) pulled out Dgrip91 and γ-tubulin from larval brain lysates
Analysis of protein synthesis by dynamic SILAC. The top 10% of proteins that are translated slower in Dnmt2−/− versus wild-type cells are indicated in orange. The top 10% of proteins that are translated faster in Dnmt2−/− versus wild-type cells are shown in blue. A change of >  twofold is indicated by the black lines.
(B) Characterization of the diameter and zeta potential (Z-potential) with the addition of each layer. Graph below presenting NP size distribution.
E) 25 cells across three independent experiments were analyzed for each condition. % of Rab10 vesicles positive with the indicated marker in each cell were quantified. Each dot represents the mean results from vesicles analyze in one cell. The group means of % Rab10 vesicles positive with the marker are shown, with error bars representing ± SEM. Significance was assessed by Mann-Whitney test for each marker, where ** representing p<0.01, **** p<0.0001 and N.S p>0.05.
(K) Ex vivo BHEL proliferation after 3d of co-culture with control or NEF-expressing CD4OT-II cells. BHEL cells were labelled with the cell proliferation dye eFluor670 and co-cultured with NGFR-enriched CD4OT-II cells expressing NEF in the presence or absence of HEL-OVA Ag. T cell-dependent B cell proliferation was assessed by quantification of the dilution of eFluor670 using flow cytometry.
H BMMΦ and MGC, from BMMΦ stimulation with LP for 6 days, were infected with BCG of indicated MOI. Cells were lysed after 72 hours and plated on 7H11 agar for CFU quantification after 3 weeks. *p < 0.05, **p < 0.01, ****p < 0.0001 (two-tailed unpaired t-test).
IDR-Screen consists of a modular set of stages that can broadly be grouped into the experimental and computational phases. A library of random or designed sequences is inserted into a genome, expressed as a part of a protein that is used for selection (survival or other readouts such as fluorescence). The library is then screened to discover sequences that are functional/non-functional based on the designed assay to infer functionality. Upon data processing, this dataset of experimentally validated functional and non-functional sequences are analyzed to learn the rules using Machine Learning (ML) approaches
(I, J) Colocalization of GFP-LC3 vesicles with the lysosomal marker LAMP1 was analysed by immunofluorescence in cells treated as in A. The number of LC3‐positive vesicles that colocalised with LAMP1 was quantified in I. Data are expressed as the percentage of LC3 vesicles per cell that are LAMP1‐positive±s.e.m., with at least 14 cells per condition. Representative images are shown in J. Arrows indicate LC3‐positive vesicles colocalizing with LAMP1. Scale bars=10 μm.
Principal component analysis of HuES6 ESCs, 393.2 iPSCs, d2 PGC‐precursor cultures, and FACS‐sorted PGCLCs.
D GFP‐Atg11, GFP‐Atg11 hrr25‐ts, and GFP‐Atg11 atg19Δ cells containing BFP‐Ape1 and Cup1‐Ape1 were grown to log phase. Overexpression of Ape1 was induced by addition of 250 μM CuSO4 for 3 h. coloc.: Cells with GFP‐Atg11/BFP‐Ape1 co‐localization. n = 50 (wt), 84 (hrr25‐ts), 127 (atg19Δ). Scale bar, 3 μm.
(B) Diffusion map, displaying the first three DCs, generated from the miRNA expression profiles reconstructing the developmental trajectories of the αβ and γδ developmental lineages across human thymocyte subsets. The line connecting the different subsets is reflecting the developmental stages of human T cell development.
(C) Loss of viability during starvation. Wild‐type (KA311B, ○), apg12Δ (YNM101, ●) and apg16Δ cells (YNM124, ▴) were cultured in nitrogen starvation medium, and their viability was determined by phloxine B staining.
F. The total weight of the extramuscular fat, including posterior subcutaneous fat, mesenteric fat, and retroperitoneal fat.
C, RAW 264.7 were incubated with or without Akt inhibitor IV for 1 h prior to challenge with T. gondii. Monolayers were examined by light microscopy 2 h and 24 h post-challenge.
(F) Representative images of low, medium, high protein expression of LKB1 in human lung adenocarcinomas. Scale bar, 150 μm (top), 50 μm (bottom).
(A) Relative transcripts of components of Notch signaling, Wnt signaling, Hedgehog signaling pathway in IMA tumors of KLN group relative to KL mice (n=4 per group). Results are mean ± SD. Significance was calculated by two-tailed unpaired Student's t-test with Welch's correction. **p=0.0048 (Hes1), ***p=0.0003 (Hes5), **p=0.0051 (Hey1), **p=0.0025 (Hey2), *p=0.0110 (Ccnd1).
(C) Representative images showing expression of pAhR in MC38 cells and Caco2 cells treated with MBELNs from three biological replicates. Scale bar 20 μm.
(A) Motif-wise combinatorial mutations within the core promoter: motif strength and motif position are changed individually. From top to bottom: knockout of motifs (individual or pairwise knockout of motifs, and knockout of all motifs); replacing the original motif with its computationally (XXmotif) derived sequences with different PWM scores (consensus with the highest score), or insertion of the consensus into the motif-less promoter sequences; point mutation of motifs; substitution with functionally or positionally equivalent motifs from other architectures; shift of motif positions; sequence context exchange between different core promoters. The Mec2 motif composition is shown here as an example.
F. Western blot analysis of mTORC1 activity in Aster-C KO cells stably re-expressing exogenous GFP-Aster-C under nutrient starvation and AA stimulation. Aster-C KO cells were transfected with GFP-Aster-C and selected with G418 for 2 weeks.
Scatter plots showing individual recordings of pairs of uninfected and infected neurons in slices at −60 mV (AMPAR-mediated EPSCs; C) or at +40 mV (NMDAR-mediated EPSCs; D). Error bars represent SEM. Statistical significance was calculated according to the Wilcoxon signed-rank test. Quantification of individual (open circles) and average (grey bars) AMPA/NMDA ratios of neurons from uninfected and infected slices, where AMPAR-mediated current is taken as the peak response at −60 mV, and NMDAR-mediated current is measured at +40 mV at a latency of 60 ms following stimulation. Error bars represent SEM. Statistical significance was calculated according to the Mann-Whitney U test. F, G. As C, D, for GSK3β. Error bars represent SEM. Statistical significance was calculated according to the Wilcoxon signed-rank test. H. As E, for GSK3β. Error bars represent SEM. Statistical significance was calculated according to the Mann-Whitney U test.
WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) show total Tau (1st blot), serine 396 p-Tau (2nd blot), threonine 231 (AT180, 3rd blot) and serine 199 p-Tau (AT8, 4th blot) relative to actin (N = 7).
a Differential gene expression analysis shows a set of 196 genes being regulated by CHIR in d4TCF cells; several of these changes only appear when TCF/LEF proteins are not present (dark green set). Of the 134 genes that are not regulated by CHIR in dBcat cells (putative β-catenin-dependent genes), 107 require the removal of TCF/LEF factors, in that their regulation only occurs in d4TCF cells. The other 27/134 β-catenin-dependent transcriptional changes match the TCF/LEF-independent target genes previously described in Figure 3a. Their regulation occurs both in the presence and in the absence of TCF/LEF factors. 90/107 of the putative β-catenin-dependent genes, stop being regulated by CHIR in pentaKO cells (β-catenin-GHOST, blue box)
F) Fluorescent micrographs of four cell embryos of WT or zsp-1(gg682) expressing the indicated fluorescent proteins. Scale bar, 5μm.
(B) Representative H&E and IHC staining for NANOG in human ADC and IMA. Scale bar, 50 μm.
H Responsiveness of undifferentiated (undiff) and 3- or 8 days PMA differentiated (ddi) THP1 cells to Sa19 challenge (n = 3).
In our hypothetical model, Rab10 is initially recruited to PI(3,4) P2 /PI(3,4,5) P3 positive membrane ruffles at the early stage of macropinosome formation. The factors that underlie Rab10-patched recruitment to these initial membranes are not known. During the process of full ruffle closure, PI(3,4,5) P3 is concentrated on macropinosomes, with Rab10 now recruited at much higher levels to facilitate early trafficking of macropinosomes. Now distinct form the plasma membrane, without LRRK2 phosphorylation, Rab10 binds EHBP1L1 to facilitate the formation of tubular endosomes which mediate fast recycling of surface receptors. Our antibody staining demonstrates that virtually all macropinosomes (defined by 70 kDa dextran positivity) in the cells studied here included the GPCR CCR5 and integrins (CD11b). The fate of recycling-tubular endosomes is likely dictated by EHBP1L1 effectors and the local microcytoskeleton network. On the other hand, if LRRK2 phosphorylation of Rab10 occurs on Thr73, EHBP1L1 interaction is weakened and instead RILPL2 interaction is promoted. The net effect may be to inhibit EHBP1L1-mediated fast recycling of CCR5 to retain an endosome-localized activated receptor complex. In vesicle maturation, the former macropinosomes assume early and then late endosome markers. These endosomes, if loaded with CCL5-bound CCR5, appear to potently activate Akt signaling pathways using these PI(3,4,5) P3 enriched vesicles as a platform. Through this signaling axis, critical pathways that mediate chemotaxis, as well as other possible pathways not studied here including cell survival in tissues and respiratory bursts, may be promoted (through LRRK2 phosphorylation of Rab10).
(B) De-repression of predicted ssc-miR-205 targets. In three independent microinjection experiments, ssc-miR-205 was inhibited by a microinjected antisense oligonucleotide inhibitor and target levels were assessed 24 hours after microinjection by RT-qPCR. Error bars = SD. Data information: asterisks indicate statistical significance (p-value) of one-tailed t-test, (*p < 0.05, **p < 0.01, ***p < 0.001).
(i,j) Immunoblots of brain lysosomes incubated with LRRK2 and increasing concentrations of GAPDH (i) or RNase A (j). All values are mean + s.e.m.; differences with lysosomes incubated with the protein alone were significant at *P 0.05, unpaired t-test. Full-length blots and gels in Supplementary Figure 12.