EMBO/sd-character-level-ner huggingface dataset:
Figure 4Three-dimensional feature engineering from molecular properties. Initial properties that can be determined only with an atomic resolution structure, in the context of an amino acid sequence, or that depend only on amino acid identity are denoted at left. This property list is a non-redundant abbreviated set of all properties considered (see Appendix Table S4 and Materials and Methods for full detail). Columns of the feature matrix at right are alternating property sums and means at spatial scales denoted below matrix. p = a molecular property; i = RKPT residue; k = neighbor residues of i; r = radius length. See also Fig EV3.   Sequence-homology-based features for machine learning were derived by performing sequence alignments of all RKPT sites (+/- 10 residues) anchored at the central residue to compute alignment scores that were then reduced to a computationally manageable number of features by principal component analysis (PCA).
Figure 4A. Parasites overexpressing EK-GFP or its S37A mutant were synchronized and parasitemia was determined at the end of first (48 h.p.i) and second cycle (96 h.p.i). Fold change in parasitemia of EK_S37A parasites with respect to WT EK overexpressing parasites was compared, which was significantly reduced (mean± SEM, n=3; biological replicates, *p<0.05, ANOVA). B. Giemsa stained thin blood smears prepared at indicated hours post-infection (h.p.i) from assay. Arrows indicate parasites exhibiting abnormal morphology, which were observed at the beginning of each replication cycle. C. IFA was performed on parasites expressing WT EK-GFP or its S37A mutant 6-12h post-invasion to detect (i) RAP1, which is transferred to PV post invasion, and (ii) MSP1 which is located at the PVM. Parasite expressing WT EK-GFP exhibited typical round ring like shape. In contrast, several parasites expressing the S37A mutant exhibited irregular morphology with much smaller vacuolar space and in some parasites RAP1 was found outside the PV (Scale bar-1 μm). D. Quantitation of abnormal parasites in IFA described in panel C (mean± SEM, n=3; biological replicates, ***p<0.001, t-test). E. Parasites EK-GFP or its S37A mutant were synchronized and parasites were allowed to mature to schizonts/segmentors. The graph shows average number of merozoites per schizont from three biological replicates. Each replicate represents an average of merozoites from 30-40 schizonts. (mean± SEM, n=3; biological replicates, *p<0.05, t-test).
Figure 5A. 3D7 parasites were treated with DMSO or 50nM MMV048 for 24h. Subsequently, parasites were fixed and IFA was performed to detect ER marker BiP and PfCDPK7. While PfCDPK7 was present in puncta proximal to ER (left panel), inhibitor treatment caused a loss in this vesicular localization and resulted in a more diffuse distribution of the enzyme (right panel) (Scale bar-1 μm). B. Western blotting was performed on parasites treated with DMSO, 10nM UCT943 or 50nM MMV048 as described above using anti-PfCDPK7 or anti-Actin (loading control) antibody. C. 3D7 parasites were treated with DMSO or 50nM MMV048 for 20-24h. Subsequently, IFA was performed ~24h post-invasion to detect RAP1 and MSP1 (left panel) Right panel, Quantitation of parasites exhibiting abnormal staining for RAP1 outside the PV was observed (mean± SEM, n=3; biological replicates, **p<0.01, t-test; Scale bar-1 μm).
Figure 2A. Schematic depiction of mapping scenarios from updating chemoproteomic-detected protein sequences using stable or versioned identifiers. B. Distribution of number of isoforms per stable UniprotKB ID for 3,953 detected proteins. C. Frequency of specific isoform name for 2,487 multi-isoform UniProtKB canonical proteins. D. Schematic depiction of glucose-6-phosphate dehydrogenase (G6PD, UniProtKB ID P11413) cross-referencing both identical and non-identical sequences of Ensembl Stable IDs from five releases. E. Heatmap of protein sequence distance scores for detected UniProtKB and cross-referenced Ensembl proteins from five releases. Each gene name corresponds to one unique stable Ensembl protein ID.
Binding of Atg18Sloop and Atg18Dloop to small unilamellar vesicles.Figure 5Binding of recombinant Atg18 variants to liposomes. SUVs were made of EPC with 5% of the indicated phosphoinositides, or of EPC and the indicated fraction of PS. Cholesterol had been added to 20 mol% of the total phospholipid amount. Liposomes were incubated with the purified proteins for 30 min at room temperature (25°C), centrifuged and the supernatants (S) and pellets (P) analyzed by SDS-PAGE and Coomassie staining. Binding is shown for a, Atg18wt Binding of recombinant Atg18 variants to liposomes. SUVs were made of EPC with 5% of the indicated phosphoinositides, or of EPC and the indicated fraction of PS. Cholesterol had been added to 20 mol% of the total phospholipid amount. Liposomes were incubated with the purified proteins for 30 min at room temperature (25°C), centrifuged and the supernatants (S) and pellets (P) analyzed by SDS-PAGE and Coomassie staining. Binding is shown for b, Atg18FGGG; Binding of recombinant Atg18 variants to liposomes. SUVs were made of EPC with 5% of the indicated phosphoinositides, or of EPC and the indicated fraction of PS. Cholesterol had been added to 20 mol% of the total phospholipid amount. Liposomes were incubated with the purified proteins for 30 min at room temperature (25°C), centrifuged and the supernatants (S) and pellets (P) analyzed by SDS-PAGE and Coomassie staining. Binding is shown for c, Atg18DLoop; Binding of recombinant Atg18 variants to liposomes. SUVs were made of EPC with 5% of the indicated phosphoinositides, or of EPC and the indicated fraction of PS. Cholesterol had been added to 20 mol% of the total phospholipid amount. Liposomes were incubated with the purified proteins for 30 min at room temperature (25°C), centrifuged and the supernatants (S) and pellets (P) analyzed by SDS-PAGE and Coomassie staining. Binding is shown for d, Atg18SLoop. e, The bands from a-d were quantified from 3 independent experiments. The mean with SEM is shown.
The APR-mediated aggregation process and its attenuation by aggregation GateKeepers (GKs).Figure 1A-D (a) In native protein structures, APRs (red) are usually buried within the hydrophobic core, rendering them harmless (structure adopted from PDB-entry 2AC0). Exposure of these APRs however (b), can lead to formation of highly stable aggregated species (c & d, structure adopted from PDB-entry 2M5N) that are detrimental to both protein function and cellular viability. Aggregation GKs (R, K, E and D, green) decrease APR-mediated aggregation tendency through charge repulsion. In doing so, GKs alleviate the threat posed by APRs and push the balance towards the native fold as indicated by the green arrows.
Figure 2A, B: Effect of FIP3 silencing on Rac1 expression. Jurkat cells were transfected with control, FIP3.1 or FIP3.2 siRNA. Three days later cells were lysed and the expression of FIP3, Rac1 and β-tubulin analyzed by western blot. The intensity of bands corresponding to FIP3 and to Rac1 was quantified by ImageJ and normalized to the β-tubulin band used as loading control. The mean ± SD of the percentage of band intensity in silenced cells with respect to controls of three independent experiments is shown. B: Rac1 interaction with FIP3: HEK293T cells were transfected with GFP, GFP-FIP3 WT or GFP-FIP3I738E expression vectors. 24 h later, cells were lysed and immunoprecipitated with anti-GFP Ab. Immunoprecipitates were analyzed by electrophoresis and western blot using anti-GFP Ab (top panel) or anti-Rac1 Ab (bottom panel). Total cell lysates were analyzed (100,000 cells). The position of Rac1 (20 kDa) and Ig light chain (25 kDa) polypeptides is depicted on the right side. Arrowheads at the bottom point the bands corresponding to Rac. Quantification of bands was performed with ImageJ as the percentage of intensity with respect to the total lysate bands on the left, shown below. A representative experiment out of three carried out is shown.
Inhibition of UVRAG expression increases tumour‐cell sensitivity to chemotherapy and radiation therapy in vivo and in vitro.Figure 2(A-C) After transfection with UVRAG shRNA or control shRNA for 48 h, HL60 (A), HCT116 (B) and HeLa (C) cells were treated with doxorubicin (Doxo, 1 μg/ml), cisplatin (Cis, 10 μm) and UV irradiation (5 min after 50 mJ/cm2) for 12 h or starvation (HBSS) for 3 h, and then apoptosis and autophagy were assayed (n=3, *P0.05). (D) Analysis of LC3 processing by autophagy in the presence or absence of lysosomal protease inhibitors pepstatin A (10 μg/ml) and E64D (10 μg/ml) after doxorubicin (1 μg/ml) treatment for 12 h. *P0.05 compared with control shRNA group. (E) After transfection with UVRAG shRNA or control shRNA for 48 h, ATG5+/+ and ATG5−/− murine embryonic fibroblasts (MEFs) were treated with doxorubicin (1 μg/ml), with or without Z‐VAD‐FMK (20 μM) for 12 h, and then apoptosis was assayed (n=3, *P0.05). (F) Nude mice were inoculated with 4 × 106 HL60 tumour cells following transfection of control (shControl) or UVRAG (shUVRAG)‐specific shRNA and treated with doxorubicin (10 mg/kg) beginning at day 7. Tumours were measured twice weekly, and volumes were calculated for 21 days (n=10, *P0.05; shControl+Doxo compared with shUVRAG+Doxo). (G) On day 21 in the experiments described in (F), apoptosis and UVRAG expression in tumour samples were assayed by TUNEL or western blotting, respectively (n=10, *P0.05). BAX, BCL2‐associated X protein; HBSS, Hank's Buffered Salt Solution; LC3, light chain 3; shRNA, short‐hairpin RNA; TUNEL, terminal deoxytransferase uridine triphosphate nick end labelling; UV, ultraviolet; UVRAG, ultraviolet irradiation resistance associated gene.
Fig.Figure 5A Protein expression of SQLE in human liver tumors (C) and non-cancerous adjacent tissue (N) were analyzed by western blotting. B SQLE gene expression in HCC and adjacent normal tissue was analyzed in TCGA Liver Hepatocellular Carcinoma (normal [n=50] versus tumors [n=371]). C SQLE gene expression in COAD and adjacent normal tissue was analyzed in TCGA Colon Cancer (normal [n=41] versus tumors [n=286]). p53+/+ HepG2 cells were stably overexpressed SQLE or vector control. Cell proliferation (D) are shown respectively. p53+/+ HepG2 cells were stably overexpressed SQLE or vector control. , number of colonies (E) are shown respectively. p53+/+ HepG2 cells were stably overexpressed SQLE or vector control. cholesterol concentration (F) are shown respectively. Protein expression was analyzed using western blotting (F bottom panel). G and H p53+/+ HepG2 cells transfected with control siRNA or SQLE siRNA were cultured in LDPS medium containing 5μg cholesterol for six days as indicated. Cell number (G) and cholesterol concentration (H) were determined. Protein expression was analyzed by western blotting after siRNA transfection 48 hours (G bottom panel). I p53+/+ HCT116 cells transfected with control siRNA or SQLE siRNA for 48 hours and then cells were cultured in LDPS medium containing 5μg cholesterol for 6 days as indicated. Cell proliferation is shown. Protein expression was analyzed by western blotting after siRNA transfection 48 hours (bottom panel). J - M p53+/+ HCT116 cells (J and K) and p53+/+ HepG2 cells (L and M) were transfected with SQLE siRNA or control siRNA in the presence or absence of exogenous SQLE cDNA for 48 hours. Cholesterol concentration (upper panel) and protein expression (bottom panel) were determined (J and L). Cell proliferation is shown (K and M).
Figure 3A. Immunodetection of BES1-CFP from heat-stressed plants, treated with ABA or Fluridone (Flu). 35S:BES1-CFP plants were treated for 24 hours with DMSO (control), 5 μM ABA or 10 μM Fluridone and heat-stressed as follows: lane 1: untreated control; lane 2: 45°C for 30 minutes; lane 3: 45°C for 60 minutes. The non-phosphorylated BES1 bands were quantified with ImageJ and the obtained values are shown in blue. B. Basal and acquired heat stress resistance of abi1tM. For basal resistance assays (top) plants were directly exposed to 45°C for the indicate time. For acquired resistance (bottom), plants were primed with the respective temperatures for 120 minutes before transfer to 45°C for 150 minutes. Data show the mean ±SE. n=7. The asterisks indicate significant differences compared to wild-type by Student's t-test (*P≤0.05; **P≤0.01 C. Immunodetection of native BES1 from heat-stressed and epiBL-treated abitM plants. abitM and wild-type plants were grown on ½ MS medium either containing DMSO as a control or 1 μM epiBL and either left untreated or exposed to 45°C for 60 minutes. The non-phosphorylated BES1 bands were quantified with ImageJ and the obtained values are shown in blue.
Figure 2(A) μCT images of the spine in PGIS model (2D and 3D reconstruction). Arrow head shows spinal ankylosis. n=5 per group. μCT images of new bone (red area) in hind paws (2D and 3D reconstruction) in DBA/1 model compared to baseline.   (B) Incidence of spinal ankylosis in PGIS model. n=5 per cage of total 3 cages per group, Fisher's exact test. (C) Quantitative analysis of structural parameters of spinal ankylosis by μCT analysis. n=5 per group, one‐way ANOVA, Bonferroni post hoc. (D) RT-qPCR analysis of expression of CaSR in spinal ligament tissuse. n=3, Student's t-test. (E) H&E, SOFG and Immunofluorescence analyses of the spine specimen of PGIS model compare to baseline. n=5 per group.(G) H&E, SOFG and Immunofluorescence analyses of the spine specimen of PGIS model at 30 Weeks compare to baseline. GP: Growth plate. n=5 per group.
Figure 6A-B. 3D7 parasites were synchronized and treated with 10nM UCT943 or 50nM MMV048 for 10-12h. Subsequently, parasites were incubated with 14C-Cho (A) or 14C-Eth (B) and were harvested after 12h. Total lipids were extracted and separated by TLC. The radiolabeled lipids were detected by phosphorimaging and quantitated by densitometry (upper panel). Bottom Panel (A and B), fold change in PC and PE formation in inhibitor treated parasites with respect to DMSO treatment was determined (mean±SEM, n=4; biological replicates, **p<0.01, ***p<0.001, ANOVA; ns, not significant). C-D. UCT943 and MMV048 treated 3D7 (C) or EK-GFP overexpressing parasites (D) were subjected to Western blotting using anti-PMT (C) and anti-GFP (D) antibodies (left panels). Right Panels: densitometry was performed for bands corresponding to PMT (C) or EK-GFP (D), which were normalized with respect to Actin. Fold change in PMT or EK was determined with respect to DMSO treated parasites (Mean± SEM, n=4; biological replicates, *p<0.05, ***p<0.001, ANOVA).
Figure 2A. A549 cells were treated with IFN-α (100 U/mL), IFN-λ (200 ng/mL) or IFN-γ (10 U/mL) for 6 hrs after which they were infected with ZIKV (MOI=3) for 18 hrs (Pre-treatment). Alternatively, cells were first infected with ZIKV for 6 hrs followed by treatment with IFN for 12 hrs (Post-treatment). Total RNA was isolated and levels of ZIKV genomic RNA were determined by qRT-PCR. Values are expressed as mean ± standard error. *P<0.05, **P<0.01 (Student's t-test); N=3 B. A549 cells were infected with ZIKV (MOI=3) for 6 hrs prior to addition of IFN-α (100 U/mL), IFN-λ (200 ng/mL) or IFN-γ (10 U/mL) for 12 hrs. Total RNA was isolated and levels of ifit1 RNAs were determined by qRT-PCR. Values are expressed as mean ± standard error. *P<0.05, **P<0.01 (Student's t-test); N=3 C. A549 cells were infected with ZIKV (MOI=5) for 6 hrs and then transfected with ISRE- or GAS- promoter-driven firefly luciferase together with a constitutively active renilla luciferase construct. Sixteen hours later, cells were treated with IFN-α (100 U/ml) or IFN-α (10 U/ml) for 2 hrs. Cells lysates were harvested and relative luciferase activity from ISRE- and GAS-promoters were determined. Values are expressed as mean ± standard error. *P<0.05 (Student's t-test); N=3 D. HEK293T cells were transfected with ZIKV protein expression constructs together with an ISRE promoter-driven firefly luciferase plasmid (pGL3B/561) and a constitutively active renilla luciferase construct (pRL-TK). After 24 hrs they were treated with IFN-α (100 U/mL) for 10 hrs. Cell lysates were then harvested and subjected to luciferase assays. C = capsid; E = envelope. Values are expressed as mean ± standard error. *P<0.05 (Student's t-test); N=3
Figure 6A) Microtubules perturbations impact the trancriptome of differentiating cells. Volcano-plot representation of down-regulated (blue) and up-regulated genes (red) in non-treated/control cells relative to ciliobrevin-D treated cells. Each circle represents the fold change (FC) of the quantity of mRNA and the significance of the change based on three independent replicates. Expressed genes with a false discovery rate (FDR) lower than 0.05 are shown in grey, whereas genes with a FDR greater than 0.05 are shown in blue or red. Genes significantly mis-regulated i.e. with an absolute value of FC higher than 1.8 are shown as full disks. Names of genes of interest are indicated within the graph. Genes that are in the signature of the myeloid-differentiation pathway are shown in magenta. Genes that are the signature of the megakaryocyte-differentiation pathway are shown in green. B) Heatmap representation and hierarchical clustering of gene expression changes between non-treated and ciliobrevin-D-treated cells collected from 3 donors in each condition. The color code corresponds to a log2 scale of the differential expression levels.
a) Wild-type yeast cultured in S(-NC) for 4 h.f3(a) Wild-type yeast cultured in S(-NC) for 4 h. PtdIns(3) P was labelled intensely in the EF of autophagosomal membranes. A lower but still significant amount of labelling was also seen in the PF of autophagosome membranes as well as in the EF of the vacuolar membrane. Scale bar, 0.5 μm. (b) Autophagosomes in wild-type yeast cultured in S(-NC) for 4 h. The autophagosome was identified as a smooth-surfaced double-membrane structure, and seen in two different patterns, as shown in the diagrams in c. Upper panel: convex structures displaying the outer membrane EF and the inner membrane PF. Lower panel: concave structures displaying the outer membrane PF and the inner membrane EF. In both cases, PtdIns(3) P was labelled more intensely in the EF than in the PF. Scale bars, 0.2 μm.
Figure 2A. MS-phospho-proteomics analysis of RCS with indicated genotypes (ctrl=wild type) treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 16 hours, showing biological processes regulated by FGF signaling (in blue: up-regulated, in green: down-regulated). N=4 biological replicates were analyzed. FDR <0.05. B. Proteomic/phospo-proteomic signaling network modulated by FGF18 in chondrocytes. Red= activating phosphorylation; blue= inhibitory phosphorylation. Cubes dimensions and colors are relative to level of protein regulations. Representative western blot analysis of IRS1, p-P70S6K (T389), P70S6K, p-AKT (T308), AKT in RCS chondrocytes treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 12h. MG132 (10 μM for 6h) to inhibit proteasome (C) activity, respectively. β-actin was used as loading control. N=3 independent experiments. Bar graphs showed quantification of indicated proteins normalized to their totals. IRS1 was normalized to β-actin. Mean +/- standard error of the mean (sem). Student's paired T-test **p<0.005; *p<0.05; NS not significant. Representative western blot analysis of IRS1, p-P70S6K (T389), P70S6K, p-AKT (T308), AKT, p-cJUN (s73) and cJUN in RCS chondrocytes treated with vehicle (5% ABS) and FGF18 (50 ng/mL) for 12h. JNK inhibitor (50 μM for 12h) to inhibit JNK (D) activity, respectively. β-actin was used as loading control. N=3 independent experiments. Bar graphs showed quantification of indicated proteins normalized to their totals. IRS1 was normalized to β-actin. Mean +/- standard error of the mean (sem). Student's paired T-test **p<0.005; *p<0.05; NS not significant. E. Co-immunofluorescence of p-IRS1 S307 mouse (green) and p-S6 S240/S242 (red) ribosomal protein in IRS1-overexpressing RCS chondrocytes treated with FGF18 (50 ng/mL) for 12h. Nuclei (N) were stained with DAPI (blue). Scale bar 15 μm. Quantification analysis of p-S6 fluorescence intensity in IRS1-overexpressing vs non expressing RCS chondrocytes. Mean +/- standard error of the mean (sem) of N=3 biological replicates. n=35 cells analyzed. Student's paired T-test *p<0.05.
Figure 1Kaplan-Meier analysis of overall survival in breast cancer patients with recurrent lethal disease, classified according to p-JNK expression. p-JNK was determined by immunostaining of breast cancer samples in a tissue microarray; p-JNK low, n = 31; p-JNK high, n = 10. P value and hazard ratio (HR) were calculated by log-rank test. Immunostaining of p-c-Jun (arrows) in patient-matched breast tumor and lung metastasis. Scale bar, 50 μm. Quantification of p-c-Jun positive (p-c-Jun+) cells per tumor area in matched primary tumors and lung metastases. Boxes depict median from 12 patients with upper and lower quartiles. Quantification of p-c-Jun positive (p-c-Jun+) cancer cells within mammary tumors and matched metastases in mice injected with MDA231-LM2 cells. Immunofluorescence analysis of p-c-Jun in micrometastatic (day 7) and macrometastatic (day 21) nodules in a xenograft mouse model injected intravenously with MDA231-LM2 cells. DAPI was used to stain cell nuclei, and cancer cells express GFP as a marker. Scale bar, 50 μm. Quantification of p-c-Jun+ cancer cells Experimental setup to address the role of JNK signaling in mammary tumor progression and metastasis. MDA231-LM2 or SUM159-LM1 cells were implanted bilaterally into the fourth mammary fat pads of NSG mice. In vivo treatment with the JNK inhibitor CC-401 (JNKi) commenced at day 5 post implantation and was repeated every three days thereafter until analysis. Mammary tumor growth curves from mice described in panel G. Each value represents the mean ± SEM. For MDA231-LM2, n = 12 tumors in 6 mice for each experimental group. For SUM159-LM1, n = 16 tumors in 8 mice for each experimental group. Lung metastatic burden in MDA231-LM2 or SUM159-LM1 tumor-bearing mice treated with JNKi. Quantification of lung metastases. FOV, field of view; LS, lung section. Each value represents the mean ± SEM. For metastatic foci per FOV, 8-10 fields were quantified per mouse. MDA231-LM2 tumor-bearing mice: n = 6 mice per group. SUM159-LM1 tumor-bearing mice, vehicle n = 8 mice; JNKi n = 7 mice. Lung metastatic burden in MDA231-LM2 or SUM159-LM1 tumor-bearing mice treated with JNKi. Representative histology examples of metastasis in lungs, detected by expression of human vimentin. Scale bar, 100 μm. Experimental setup to determine lung colonization of in vivo vehicle-treated and JNK-inhibited MDA231-LM2 cancer cells after intravenous injection. In vivo treatment with JNKi commenced at the time of implantation and was repeated every 3 days thereafter until analysis at day 17. Metastatic burden determined by photon flux in lungs of MDA231-LM2-injected NSG mice treated with vehicle and JNKi. Boxes show the median with upper and lower quartiles. Whiskers represent minimum and maximum values. Vehicle control, n = 8; JNKi-treated, n = 8. Examples of bioluminescence in mice
Figure 4Structure of ryRyR1 at a resolution of 17.5 Å. Two views are through the middle slice (top) of the reconstruction and at the level of sarcoplasmic extentions 22 Å below (bottom panels). The movement of the outer domains is associated with a visible change in membrane curvature as compared to the apo-structure. This movement is highlighted by red arrows in the right panels. Scale bar: 10 nm. A volume-rendered representation of the apoRyR1 (orange) and ryRyR1 (blue) structures with the highlighted conformational changes. The ryRyR1 reconstruction was mirrored in the right panel for a clear comparison to the aporRyR1. The left panel depicts the view down onto the receptor from the cytoplasm. The right panel depicts the section through the isosurface indicated by the dashed line, with red arrows indicating the conformational transition of the SR extensions (dark-orange and blue circles for apoRyR1 and ryRyR1, respectively). Red arrows indicate the conformational changes of the SR extentions.
Figure 6Schematic representation of Cdc42-Borg4-Septin 7 axis in the regulation of HSC polarity and function.