EMBO/sd-character-level-ner huggingface dataset:
Structural constraints on the usage of GKs in the native fold.Figure 5A) Boxplots showing all-atom analysis of GK energetic contributions to a set of native folds from the E. coli cytoplasmic proteome. The upper whiskers indicate the largest value no further than 1.5 times the Inter-Quartile Range (IQR) from the upper hinge, the lower whiskers show the smallest value at least 1.5 * IQR from the lower hinge. Notches extend 1.58 * IQR / sqrt(n) from either side of the median and represent a 95% confidence interval for the median value. Grey shaded area indicates total energy associated with the placement of GKs in the native fold, the remainder of the plot shows the breakdown of this total energy into constituent energy terms. The number of observations per GK is indicated above the boxes depicting the distribution of the total energy for each of the GKs. B) Burial analysis on a set of E. coli structures of cytoplasmic, monomeric proteins. Violin- and boxplots indicate distribution of the degree of mainchain burial for each of the charged amino acids, grouped by their usage as GK. The upper whiskers indicate the largest value no further than 1.5 times the Inter-Quartile Range (IQR) from the upper hinge, the lower whiskers show the smallest value at least 1.5 * IQR from the lower hinge. Notches extend 1.58 * IQR / sqrt(n) from either side of the median and represent a 95% confidence interval for the median value. Statistical differences between charged residues flanking APRs versus charged residues elsewhere in the protein were determined through Wilcoxon test. P-values are indicated. C) Schematic representation of the approximate sidechain lengths of the four charged residues. Circles indicate a probe radius of 1.5Å used here for the determination of distance from the solvent-accessible surface. D) Fraction of sidechain buried versus cα depth bin for all charged residues in the dataset. Mean values are plotted, whiskers indicate edges of a 95 % confidence interval for the population mean based on a t-distribution. The number of observations per group is indicated. E-H) Dissection of energetic components with increasing mainchain depths for each charged residue. Mean values are plotted, whiskers indicate edges of a 95 % confidence interval for the population mean based on a t-distribution. The number of replicates per group is indicated. The numbers of observations per group are the same as those indicated in panel D. I) Analysis of an exhaustive mutational fitness screen conducted by Varadarajan and colleagues (Bajaj et al, 2005). The percentage of mutations found to be inactivating is plotted against the depth of burial in the protein core for each of the charged residues. The dotted line indicates where charge introduction becomes predominantly destabilizing. Sidechain lengths derived from panel C are indicated on the x-axis.
Figure 7A Schematic diagram of NKG2D-ligands combination and dissociation model. NKG2D binds and dissociates with multiple ligands at different initial on-rates (kon-initial) and off-rates (koff). Ubiquitous mechanical forces in vivo regulate the disassociation of NKG2D and ligands. B Probabilities of productive signals of different ligands binding with NKG2D when at forces of 0 pN, 5 pN, 10 pN and 15 pN, respectively. C Probabilities of output signals at 300s varied with force-dependent off-rates of the three ligands, MICA, MICB and ULBP3. Off-rates at different mechanical forces measured by experiments had been marked by specific symbols: pentagram, square, circle and right-pointing triangle represented off-rates at 0 pN, 5 pN, 10 pN and 15 pN, respectively. D Contour plots showed probabilities of output signals at 300s produced by continuously variable initial on-rates and force-dependent off-rates.
Figure 1(A-D) A. castellanii was infected (MOI 5) with L. pneumophila JR32 producing (A) GFP under the control of PflaA (Ptac-mCherry-PflaA-gfp) and mCherry constitutively, (B) GFP under the control of PralF (PralF-gfp) and stained with DAPI, (C) GFP under the control of PsidC (PsidC-gfp) and stained with DAPI, or (D) Timer constitutively (pNP107). The infected amoebae were fixed at different time points post-infection, analyzed by confocal microscopy and 3D reconstructed (scale bars: 5 µm). Motile and virulent bacteria (GFP-positive) emerge at the colony cluster periphery only after bacterial replication has ceased (red fluorescent Timer). (E, F) Optical section (E) (scale bar: 5 µm) and distribution of the fluorescence signal intensity (F) of A. castellanii infected with mCherry-producing L. pneumophila JR32 (Ptac-mCherry-PflaA-gfp) for 48 h. The plot profile was analyzed for an optical section in the center of an infected host cell and shows the intensity of the green and red channels, respectively (representative of n = 10). The GFP signal mainly localizes to the periphery of the bacterial cluster. (G) Transmission electron micrographs of A. castellanii infected with L. pneumophila. A. castellanii was infected (MOI 5, 42 h) with L. pneumophila wild-type strain JR32 and subjected to high-pressure freezing and electron microscopy. Many LCVs were still intact at 42 h post infection (left panel; arrow: intact LCV membrane, arrowhead plasma membrane), and occasionally, the bacteria were flagellated (middle panel, arrow). Some LCVs were already ruptured, and the bacteria were released into the host cell cytosol (right panel; arrows: ruptured LCV membrane). Scale bars: 2 µm, 0.5 µm (insets).
Figure 2(A) Animal protocol. (B) Changes in body weight relative to starting weight during 6 weeks (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. (C) Left, representative images of duodenal damage by H&E staining. Scale bar: 200 μm. Right, graph depicted the ratio of the morphometric assessment of villus height to crypt depth (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.. (D) Western blot and densitometry analyses of duodenal tight junction proteins (claudin-1, occludin, ZO-1 and ZO-2; n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.. (E) Western blot and densitometry analysis of duodenal zonulin (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.. (F) Intestinal permeability was assessed by measuring FITC-dextran (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons..
Figure 8ITC titration curves and relative heats of binding for (A) cAMP binding to Bd1971ΔEAL. Successive injections of 6 µl of cNMP (0.5 - 1.6 mM) were made into 1.4 ml of apo-Bd1971ΔEAL (50 - 150 µM) and heat changes measured. The top panels show the ITC titrations and the bottom panels show the binding isotherm associated with each ITC experiment. ITC titration curves and relative heats of binding for cGMP binding to Bd1971ΔEAL. Successive injections of 6 µl of cNMP (0.5 - 1.6 mM) were made into 1.4 ml of apo-Bd1971ΔEAL (50 - 150 µM) and heat changes measured. The top panels show the ITC titrations and the bottom panels show the binding isotherm associated with each ITC experiment.
Semi-quantitative prediction of mRNA log2 fold changes upon different signalling scenarios.Figure 4 Figure 4 - Semi-quantitative prediction of mRNA log2 fold changes upon different signalling scenarios. A: Gene expression upon different stimulations was predicted based on fitted model parameters and measured pERK2 levels. Predictions were verified with gene expression time-course data. B: Signalling input conditions (left side shows deduced input function, right side shows pERK2 measurements): Sustained ERK signalling (4OHT), two-hour pulse ERK signalling (4OHT+U0126), growth factor signalling (EGF: Epidermal growth factor, FGF: Fibroblast growth factor). Deduced input functions: 100% signalling amplitude corresponds to mean induction in training condition (4OHT). Growth factor-induced input functions are linear interpolations of pERK2 log2 fold changes relative to mean induction in test condition. C: Predictions are verified with actual gene expression data. Heat maps show log2 fold changes of induced mRNAs. P: Model prediction. D: Gene expression data. E: Mean error = mean of absolute residuals.
Figure 3Relationship between area and polygon distribution. A) Area distribution of several Voronoi diagrams along the CVT path. Cell areas became progressively more homogeneous after each Lloyd iteration B) Comparison of area distribution for proliferating epithelia cNT (blue), dWL (green) and dWP (red). At the right of the image Biceps (green) and Diagram 5 (grey) images.
ALKAL2 collaborates with MYCN to drive NB in mouse models.Figure 4A. The oncogenic activity of MYCN is potentiated by overexpression of ALKAL2. Kaplan-Meier survival curves for Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN mice. Also shown are Rosa26_Alkal2N, Alk-F1178S and control (Ctrl) mice. Comparison of survival of Th-MYCN alone and Rosa26_Alkal2;Th-MYCN curves showed a significant difference (p=0.003; log-rank test). Tumours harvested from Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN mice express NB markers. Tumours from all three genotypes were large, in most cases filling the abdominal cavity (B). Dissection post-mortem revealed that the majority of Rosa26_Alkal2;Th-MYCN (18/20) and Alk-F1178S;Th-MYCN (7/10) tumours did not involve the adrenal glands (C). Histological examination of Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN tumours revealed positive staining for NCAM1, synaptophysin (SYP) and Chromogranin A (CGA). Scale bars indicate 100μm. (D) Histological examination of Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN tumours was confirmed for NCAM1 and SYP along with MYCN, ALK and ALKAL2 by immunoblotting (E). Immunoblots are representative of 3 independent technical analyses. F. Accumulated Kaplan-Meier survival curves are shown for all monitored Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN mice over time, estimating tumour penetrance (p<0.001; log-rank test).
Epithelial topology becomes increasingly regular as the early egg chamber matures.Figure 1A) Egg chambers expand and elongate through development. This is acheieved through collective migration (A") of t B) Egg chambers flatten along the coverslip, allowing for follicle cell morphologies to be compared in two dimensions. In (B), three live w1118 (control) egg chambers expressing the membrane marker Basigin::YFP are shown in multiple planes of focus, with a z-reconstruction at the bottom. Because the egg chambers flatten at the coverslip, the basal follicle cell morphologies can be revealed in a single focal plane. To account for differences in follicle cell height between the three egg chambers, which increase in maturity from left to right, separate focal planes are shown for the apical morphologies. A diagram illustrating the position of the three focal planes with respect to the flattened egg chamber is shown in (B"). Scale bars = C-E) Follicle cell cross-sectional area decreases (C) and cell shape becomes more regular (D) and hexagonal (E) as early-stage egg chambers mature. These measurements were derived from at least three egg chambers from at least three flies per AR range. Bars in (C) and (D) represent mean and standard deviation. Statistical significance for cell side distributions was calculated using a chi-squared test. Number of cells used for morphological analysis: 1.0-1.2 apical n=23, basal n=27; 1.2-1.4 apical n=114, basal n=61; 1.4-1.6, apical n=160, basal n=149. Vertex counts: 1.0-1.2 apical n =38, basal n=33; 1.2-1.4 apical n=73, basal n=70; 1.4-1.6, apical n=284, basal n=259.
Figure 1A) Alignment of sequences of all human α- and β‑tubulin isotypes. Only the C-terminal tail region of the tubulins are shown. Isotypes with identical amino acid sequence in these regions are pooled. A large number of glutamate residues in the C-terminal tails would, if modified by glutamylation, be detectable with GT335 (yellow), which requires one additional acidic amino acid residue after the modification site (Wolff et al, 1992). By contrast, the GEF motif (red/purple), which is the main glutamylation site in β2‑tubulin (TUBB2) in the brain (Rüdiger et al, 1992), is present only in a few β‑tubulin isotypes, but not in α-tubulin. B) Schematic representation of the synthetic peptide used as antigen to raise the β-monoE antibody. The modified glutamate residue is in red. C) Representative immunoblots of brain extracts of wild-type, Ttll1-/- and Ttll7-/- mice. Polyglutamylation of α-tubulin, detected with polyE and GT335, is specifically lost in Ttll1-/- brain. By contrast, β-tubulin glutamylation, which is specifically detected with β‑monoE, is absent from brains of Ttll7-/- mice. D) Representative immunoblots of extracts of wild-type, Ttll1‑/- and Ttll7-/- primary hippocampal neurons at DIV4. As in brain (C), α-tubulin polyglutamylation is specifically lost in Ttll1-/- neurons, while β-tubulin glutamylation lacks in Ttll7-/- neurons. E E) Schematic representation of the epitopes detected by the anti-glutamylation antibodies used in this study. For clarity, α- and β‑tubulin are shown separately. F,G) Immunocytochemistry of DIV4 primary hippocampal neurons from wild type, Ttll1-/- and Ttll7‑/- mice. Microtubules in Ttll1-/- cells have reduced levels of polyE signal, indicative of lower α-tubulin polyglutamylation (F), Ttll7‑/- neurons are specifically reduced in β‑monoE reactivity, indicating the lack of β‑tubulin glutamylation (G).
Figure 7Confocal images of IHC and OHC hair bundles of Clrn2clarinet/clarinet mice and heterozygous littermates at P6 immunostained for PDZD7 (A, green) and whirlin (B, green) and actin (red in both figures). The PDZD7 immunostaining is normally restricted to the base of stereocilia in both Clrn2clarinet/+ and Clrn2clarinet/clarinet P6 mice (A). Whirlin immunostaining is properly located at the stereocilia tips of IHC and OHC hair bundles (B). Harmonin-b immunostaining in IHC hair bundles. In Clrn2clarinet/clarinet mice (D), the harmonin-b immunoreactive puncta (green) were still observable on the stereocilia, but unlike in age-matched heterozygote littermates (C), were located much closer to the tip of stereocilia. The two diagrams in (C) and (D) illustrate the position of harmonin-b immunostaining (green) corresponding to the site of the upper attachment point of the tip link (UAPTL), facing the tip link. The bright green signal outside stereociliary bundles are non-specific. The change of harmonin-b localization along the stereocilium in Clrn2clarinet/clarinet mice is illustrated further by line scan (E) and quantification (F) analyses. The insets in (E) show images of individual stereocilia used for the line scan signal analysis. The harmonin-b immunoreactive puncta were located within 850 ± 28 nm distance from the tip of the tallest stereocilia in Clrn2clarine/+ mice (n=31 hair bundles from 5 mice) (F), and within 575 ± 23 nm in Clrn2clarinet/clarinet mice (n=35 hair bundles from 5 mice). Cochlear whole-mounts from P21 clarinet mice, labelled with the IHC pre-synaptic ribbon marker Ribeye (red) and the post-synaptic density marker GluR2 (green), showing a similar number of total and matched Ribeye-positive and GluR2-postive puncta in Clrn2clarinet/clarinet mutant cochleae compared to Clrn2clarinet/+ littermates, which is reflected in puncta counted per five hair cells (H) n = 4 per genotype.
Figure 3A.-F. Equilibrium dissociation constants (Kd) of protein ligands (as indicated) for SecYEG-IMVs with or without SecA or its derivatives or SecB. Data analyzed by non-linear regression and average values with standard mean error (SEM) are shown; n= 6-9 biological replicates.
Figure 5A: GO analysis of biological processes among Group IV target genes, showing enrichment of networks in the endothelial-hematopoietic transition. B: Heat map showing bona fide HSC regulators in Group IV target genes. C: Heat map showing the most depleted shRNAs in pair-wise comparisons between the D20LSK and D20LK populations. D: Validation of the involvement of Group X target genes Lrsam1, Ap2a1, Mettl22, and Hal in zebrafish hematopoiesis by MO-mediated knockdown. Whole-mount in situ hybridization of Runx1 and c-Myb expression is shown at 26 hpf and 30hpf, respectively. Prdm16 knockdown serves as a positive control. Note that nonspecific staining for Runx1 and c-Myb was largely unaffected by targeted MO knockdown, whereas HSC markers Runx1 and c-Myb staining were notably reduced in discrete cells in the ventral region of the dorsal aorta (arrows). Scale bar = 100 µm.
Validation of compartment-specific regulations.Figure 3(A) Real-time quantitative PCR (RT-qPCR) of transcripts changing differentially between compartments using the compartmentalized cultures after 48 hours PTX-treatment. n=8 independent biological replicates (except for Plk2 (n=7), where one measurement couldn't be performed due to insufficient cDNA); PTX-effect was assessed by three-way ANOVA followed by Tukey's post-hoc multiple comparison test; *p < 0.05; **p < 0.01. (B) Representative images of single-molecule FISH (smFISH) in either control or 48 h PTX-treated rat hippocampal neurons (DIV20) using probes specific for Add2, Dnajc6 and Sort1 (green). MAP2 immunostaining (red) was used to visualize neuronal somata and dendrites. Inserts at higher magnification illustrate PTX-dependent changes in dendritic RNA puncta. Scale bar = 10 μm. (C) Quantification of B. (n=3-4 independet biological replicates with 8-10 cells averaged per condition and replicate; two-sample Student's t-test; *p < 0.05; **p < 0.01). B
USP45 deubiquitylates ERCC1HEK293 cells were treated with the proteasome inhibitor lactacystin (5 μM) or bortezomib (10 μM) for the times indicated.Figure 4A HEK293 cells were treated with the proteasome inhibitor lactacystin (5 μM) or bortezomib (10 μM) for the times indicated. Cells were lysed in the presence of 0.1 M N‐ethylmaleimide to inhibit deubiquitinylation and lysates were subjected to immunoblotting with indicated antibodies. B Wild‐type (WT) and USP45 knockout (KO) U2OS cells were lysed and subjected to immunoblotting as in (A). C USP45 KO U2OS cells were transiently transfected with a construct encoding FLAG‐ERCC1. Thirty‐six hours post‐transfection cells were treated with lactacystin (5 μM) for 6 h and lysed with a buffer containing 0.1 M N‐ethylmaleimide. Flag‐ERCC1 was immunoprecipitated and treated in the absence or presence of 0.1 μg of recombinant USP45 wild‐type (WT), non‐ERCC1‐binding USP45 [Asp25Ala, Glu26Ala] (AA) or catalytically inactive USP45 [Cys199Ala] (CA) for 1 h. The reactions were terminated by addition of sample buffer and analysed by immunoblot and Coomassie staining. Similar results were obtained in at least two separate experiments.
Figure 6(a) Representative synthetic timeseries example and mathematical description of probability of differentiation (Pdiff) in relation to population mean HES5 protein levels (referred to as 'differentiation threshold', Dthresh) whereby HES5 protein abundance (P(t)) dropping below the threshold increases the rate at which cells differentiate. (b) Differentiation rates estimated from the multicellular coupled model (detailed in Figure 5) over a wide range of repression threshold values corresponding to decreasing coupling strength; three dynamic regimes are labelled as Alternating high-low, Global in phase and Local in phase mirroring examples shown in Figure 5g,i. (c) Analysis of temporal CoV and spatial CoV from synthetic data corresponding to differentiation rates shown in (b); these statistics indicate that spatial variability correlates better with differentiation rates meanwhile temporal variability shows only a moderate quasi- linear increase in Alternating high-low conditions compared to the rest.
Figure 7 Figure 7. Model for the regulation of Notch target genes by L3MBTL3. A NOTCH ICD binds to RBPJ-bound Notch-responsive elements where it builds up a coactivator complex composed of Mastermind-like 1 (MAML1) and additional co-activators to induce expression of Notch target genes. B In the absence of Notch signaling, L3MBTL3 interacts with RBPJ at Notch-responsive elements where it recruits KDM1A to repress Notch target genes. C Loss-of-function of L3MBTL3 leads to de-repression of Notch target genes.
Figure 1A. Schematic exon structure of Stim1 gene with conventional exons depicted in grey. Highlighted in red is the alternative exon 11 (named A), and additional mutually exclusive splicing of exon 13 (named L, green) or exon 13 (named B, blue). Alternative usage of 5'UTR regions are indicated with alt1 and alt2. Arrows indicate schematic location of primers, B. Schematic representation of primer annealing sites on the coding mRNA. C Analytic PCR with primers flanking the splice site using cDNA's of tissues or cells as indicated. L denotes exon L of STIM1L, A denotes additional exon A. D. qRT-PCR of exonA specific reaction normalized to sum of exon specific and wt specific (total) Stim1 (± SD) in tissues using cDNA derived from 3-4 mice. E. Schematic protein structure of STIM1 displaying functional motives. Domain A (red) is located 8 amino acids downstream of the inhibitory domain (ID, yellow) after aa 491. F. Evolutional conservation of domain A. Identical amino acids within black boxes. G. Western blot showing Stim1 and Stim1A following heterologous expression in HEK293DKO (left); right panel: quantification from 4 transfections, mean ± SD. H. Endogenous levels of Stim1 in testes from C57BL/6 wt and splice deficient 10A mice, using an antibody detecting the N-term of STIM1, detecting STIM1A (A, red arrow), STIM1 and its glycosylated (wt) and unglycosylated (wt gl.) form.
Figure 7Western blot analysis of Galectin-3 and GPNMB in the spinal cord lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p<0.001, ****, p<0.0001. Western blot analysis of Galectin-3 and GPNMB in the brain lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p<0.001, ****, p<0.0001. (E) Immunostaining of Galectin-3, CathD and CD68 in spinal cord sections from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. Scale bar = 10 µm.
Figure 5A-C. Cryo-EM micrographs of GSDMDNterm pores in E. coli extract polar lipids liposomes. The micrographs were acquired at protein/lipid molar ratios of 1/1000, 1/500 and 1/100, respectively. Black arrows indicate ring-shaped structures corresponding to oligomeric GSDMDNterm pore forms. Scale bars = 80 nm. D. Proteoliposome with protein/lipid molar ratio of 1/100 at higher magnification. Scale bar = 80 nm.
Loss of IL-2 priming correlates with reduced gene expression of some inducible genes A,B.Figure 6Relative mRNA expression levels in TB+ IL-2 and TB+ IL-2nil (A) and TB+ DMSO and TB+ Ruxolitinib (B). The expression level in the IL-2/DMSO TB+ sample is set to 1. (n=3, error bars represent standard deviation, P-values were calculated using a paired t-test with *p<0.05, **p<0.005, ***p<0.0005.) UCSC genome browser tracks showing DNase-Seq and RNA-Seq at the IL-2 regulated genes Csf2/Il3 and at the LCR within the Rad50 gene (grey box) which controls the Th2 cytokines Il13, Il4 and Il5. IL-2 pDHSs are highlighted in blue and IL-2 iDHSs in red.