EMBO/sd-character-level-ner huggingface dataset:
Figure 5Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. A. Unsupervised hierarchical clustering heat map of the 922 differentially expressed genes (DEGs) between symptomatic P. falciparum malaria and healthy immune controls using the complete method and Euclidian measure of distance. B. Mean-difference plot displaying genes differentially expressed between symptomatic P. falciparum malaria and healthy immune controls. Each gene is plotted as a single point determined by log-fold-change and average transcript abundance. Red genes are overrepresented, and blue genes are underrepresented in symptomatic malaria. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. C. Bar plots showing significantly enriched gene ontology (GO) terms scaled by Log10(P-value). Red GO terms are upregulated and blue GO terms are downregulated in symptomatic P. falciparum malaria compared to healthy immune controls. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. D. Bar plots showing significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways scaled by Log10(P-value). Red KEGG pathways are upregulated and blue KEGG pathways are downregulated in symptomatic P. falciparum malaria compared to healthy immune controls. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. E. IPA canonical pathways significantly overrepresented in DEGs between symptomatic P. falciparum malaria and healthy immune controls scaled by Log10(P-value). Pathways with a positive z-score in red are activated, and pathways with a negative z-zscore in blue are inhibited in symptomatic P. falciparum malaria compared to healthy immune controls. The ratios of DEGs found in each pathway over the total number of genes in the pathway are listed on the right. The red line corresponds to a P value of 0.05. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. F. Upstream regulator analysis of the 922 DEGs between symptomatic P. falciparum malaria and healthy immune controls. The red lines represent a significant activation z-score of ±2. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. Hierarchical clustering heatmap (G) displaying DEGs in symptomatic P. falciparum malaria and healthy immune controls predicted to be controlled by IFN-γ and IL-13 upstream regulators. Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. Spearman correlation network (H) displaying DEGs in symptomatic P. falciparum malaria and healthy immune controls predicted to be controlled by IFN-γ and IL-13 upstream regulators.
UBQLN1 acts in parallel to parkin.Fig 6(A) WT and Park2-/- BMDMs were pretreated with IFN-γ, infected with GFP-Mtb for 24h, and immunostained with the FK2 antibody. Bacterial colocalization with FK2 immunoreactivity was quantified from 2 independent experiments. (B) Park2-/- BMDMs pretreated or not treated with IFN-γ were infected with GFP-Mtb for 24h and immunostained with UBQLN1 specific antibody; Arrows indicate Mtb co-localized with UBQLN1. ns- not significant. (C) Park2-/- BMDMs were transfected with siRNA targeting UBQLN1 or control siRNA 3d prior to infection, treated with IFN-γ, and infected with GFP-Mtb for 24h prior to immunostaining for ubiquitin (FK2 antibody). Ubiquitin (FK2+) bacteria were quantified from two independent experiments. (A, C) **P<0.01, Fisher's exact test (comparing the proportion of FK2 positive bacteria in indicated samples). Results are mean +/- SEM. A minimum of 100 Mtb were counted in each experiment.
Figure 10Pah1 converts phosphatidic acid (PA) into diacylglycerol (DAG) for lipid droplet biogenesis. Ice2 inhibits the Nem1-Spo7 complex and hence Pah1. Ice2 thereby increases PA availability and relieves repression of Ino2/4-driven lipid synthesis genes, thus promoting ER membrane biogenesis. These mechanisms coordinate the production of lipid metabolic precursors and lipid synthesis enzymes.
Figure 1(A) Differentially expressed genes, as detected both in RNA-seq and microarray experiments (fold induction threshold ≥1.4). (B) Density of PRBS, defined as the total number of PR-peaks associated to each gene category (up-, down-, and non-regulated genes). PR-peaks were assigned to a gene when located from −5 Kb upstream of the TSS to the TTS (left panel) or to a window of -/+5Kb around the TSS (right panel). Peak density in the genome was calculated by considering random distribution of all PRBS in the whole genome. Data obtained after exposure to hormone for 5 and 30 minutes is shown. The p-values in comparison with the corresponding non-regulated genes are indicated. Left panel: for PRBs 5 min: *** P=1,04E-035 (UP), *** 2,40E-023 (DOWN); Right panel: PRBs 5 min: ** P=4,64E-008 (UP), * P=0.026 (DOWN). (C) Heat Maps of the PRBS associated to up- and down-regulated genes. The log2 normalized signal enrichment centered on PRBs (T0 and R5') located from −5 Kb upstream of the TSS to the TTS of up- and down-regulated genes is shown (upper panel). Lower panel: The Average profile of PRBs at R5' associated to up-, down- and non-regulated genes is depicted. (D) The graph shows the fraction of PRBs obtained after 5' of hormone as a function of the distance to a TSS of a gene up- or down-regulated (solid lines) compared to a random distribution (dashed lines). (E) Kinetics of PR binding to up- and down-regulated genes. ChIP-seq data of PR obtained after 5, 30, 60 and 360 min of hormone exposure is plotted for up, down (window: -10kb +5kb around the gene) as well as for the proximal promoters of the down-regulated genes (window: -1kb +1kb around the TSS). Lower Panel: normalized enrichment at summits (+/-50bp) of PRBS R5' using the same set as shown in upper panel.
Figure 5A, B Volcano plots showing significantly changed proteins in KO hepatocytes relative to WT in basal (A) and HBSS (B) conditions. C 2D-score plots of enriched pathways in transcriptomics analysis of KO and WT hepatocytes under basal condition and upon HBSS (2 h). D 2D-score plots of enriched pathways in proteomics analysis of KO and WT hepatocytes under basal condition and upon HBSS (2 h). E 2D-score plots of enriched pathways in proteomics versus transcriptomics analysis of KO and WT hepatocytes under basal condition. F Correlation of protein fold changes in KO in respect to WT hepatocytes under basal condition and upon HBSS (2 h). Only genes previously found in CLUH RIP experiments in HeLa cells (Gao et al., 2014) are plotted. Inset shows magnification of upper part of the graph.
Figure 8Schematic model of the current study. In an unperturbed G2 phase, cyclin F promotes the degradation of the transcription repressors E2F7/8, which leads to enhanced expression of their target genes, such as RAD51, CHEK1 and MSH2 (Left). Therefore, cyclin F dependent degradation of E2F7/8 sustains the expression of DNA repair genes before mitosis. Inactivation of cyclin F results in stabilization of E2F7 and E2F8 in G2 phase (Right). Active E2F7/8 at this stage repress the expression of DNA repair genes, leading to accumulation of DNA damage and delay cell cycle progression.
Jumpy localizes to autophagosomes.Figure 3(A) Transient association of Jumpy WT with LC3+ organelles. Time lapse sequence of C2C12 myoblasts transfected for 24 h with GFP‐Jumpy WT and Cherry‐LC3 and analysed by live confocal microscopy in a 5LIVE Zeiss microscope. EBSS was added to the cells and z‐stacks collected at 3‐min intervals for a total of 45 min. The collected images were processed to generate a maximum projection (collapsing a 3D image into an x-y projection) for each time point. Arrows indicate colocalization of GFP‐Jumpy WT with LC3. Graph: Plots of relative fluorescence intensity (GFP fluorescence pixel intensity) over time of GFP‐Jumpy WT colocalizing with Cherry‐LC3+‐positive puncta indicated by arrows. (B-I) Association of Jumpy CS mutant with autophagic organelles. C2C12 cells were transfected for 24 h with GFP‐Jumpy C330S (Jumpy CS) and tdTomato‐LC3 (LC3), fixed and immunostained with anti‐G58K (Alexa 648‐labelled secondary antibody). Jumpy CS (green), LC3 (red) and G58K (white in D, H or blue in E, I). Boxed areas (B-E) are shown at higher magnification in the corresponding panel below (F-I). Scale bars, 2 μm. White arrows indicate colocalization between Jumpy CS, LC3 but not G58K, blue arrow indicates colocalization between Jumpy CS and G58K but not LC3.
In vivo inhibition of CCR9 significantly reduces tumor outgrowth in response to adoptive TIL therapy.Figure 7A Cr-release assay showing TIL 209-mediated lysis of CCR9+ M579-A2 (transduced with control shRNA) or CCR9− M579-A2 cells (transduced with CCR9-specific shRNA). Curves represent mean ± SEM. B Scheme for the in vivo mouse experiment involving the s.c. injection of CCR9+ (shControl) or CCR9− (shCCR9) M579-A2 tumor cells in the left and right flank, respectively, of the NSG mice. Following this, at d2 and d9, mice received i.v. injection of TIL 209 in PBS (n = 7) or PBS alone (control group for tumor growth; n = 3) and measured for tumor growth. C, D Tumorgrowth curves showing mean ± SEMtumor volume of CCR9+ or CCR9−M579-A2tumors in TIL-treated mice (C) or the PBS alone group (D). Statistical difference was calculated using the unpaired one-sided Mann-Whitney U-test.
Effects of inhibiting inflammatory cell recruitment on fracture healing.Figure 4Treatment with CCR2 antagonist, INCB3344, led to impaired fracture healing compared to vehicle control as shown by the reduced % callus mineralization at day 28 after operation. Data are presented as mean ± SEM. *P = 0.011 unpaired two-sided t-test. Representative micro-CT images are shown. Scale bar, 2 mm.
Figure 3PC3, DU145 and V5-SLC1A3-DU145 cells were subjected to ASNase and TFB-TBOA treatment at indicated concentrations and cell proliferation was measured by IncuCyte assay. PC3 cells were treated under indicated conditions for 9 days and subjected to BrdU assays to determine cell cycle distributions. ASNase (0.3 U/ml), TFB-TBOA (5 μM). DU145 and V5-SLC1A3-DU145 cells were treated under indicated conditions with ASNase (0.2 U/ml) or TFB-TBOA (20μM) or both, and subjected to IncuCyte analysis for apoptotic cell counts. PC3 cells were treated under ASNase (0.3 U/ml), or TFB-TBOA (5 μM) conditions for 3 days and cell lysates were extracted and intracellular contents of aspartate, asparagine, glutamate and glutamine were determined by liquid-chromatography mass spectrometry (LC-MS). Data information: Median peak intensity was used for raw data normalization Results were calculated based on three replicates and presented as mean ± SD (unless otherwise stated). The p-value was calculated by two-tailed unpaired t test from Prism7. *p<0.05, **p<0.01, ***p<0.001. key metabolites involved in urea cycle, pyrimidine synthesis, TCA cycle, oxidation, glycolysis and carnitines metabolism were determined. The NAD+/NADH ratio of the indicated conditions was calculated and normalized to control (mean± SEM). Dash line indicates indirect effect. TCA cycle: tricarboxylic acid cycle; OAA: oxaloacetic acid; UMP: uridine monophosphate; CMP: cytidine monophosphate; PEP: phosphoenolpyruvate; NADH: nicotinamide adenine dinucleotide (reduced form); NAD+: nicotinamide adenine dinucleotide (oxidized form); NADPH: nicotinamide adenine dinucleotide phosphate (reduced form); NADP+: nicotinamide adenine dinucleotide phosphate (oxidized form); FAD: flavin adenine dinucleotide; GSSG: glutathione disulfide; HMG-CoA: 3-hydroxy-3-methylglutaryl-CoA. Data information: Median peak intensity was used for raw data normalization Results were calculated based on three replicates and presented as mean ± SD (unless otherwise stated). The p-value was calculated by two-tailed unpaired t test from Prism7. *p<0.05, **p<0.01, ***p<0.001.
OFD1 interacts with both myosin VI isoforms.Figure 1(A) List of myosin VI interactors commonly found in the four cell lines tested. (B) Total lysates from HEK293T transfected with Flag-OFD1 were IP with anti-myosin VI antibodies (1295 and 1296) and an unrelated rabbit antibody (anti-GST, as control). IB was performed with anti-Flag and anti-myosin VI antibodies. (C) Total lysates from HEK293T transfected with Flag-OFD1 or Flag (as control) were IP with anti-Flag antibody-conjugated beads. IB was performed with anti-Flag and anti-myosin VI antibodies. (D) Selected sections deriving from TEM analysis of A549 wild-type versus myosin VI KO cells. The cells were immunogold-labelled with anti-myosin VI antibody. The centrioles in the images are indicated with white dashed circles. Scale bar, 200 nm. Top: representation of the estimated localisation of myosin VI at the centrioles. (E) GST pulldown assay using the indicated myosin VI constructs or GST alone (as control) and lysates from HEK293T cells transfected with Flag-OFD1 construct. IB was performed with anti-Flag antibody. Ponceau staining as indicated. (F) GST pulldown assay using myosin VI tail (835-1295) construct (or GST alone as control) and lysates from HEK293T cells transfected with the indicated Flag-OFD1 constructs (or Flag alone, as control). IB was performed with anti-Flag antibody. Ponceau staining as indicated.
Fig.Figure 2A. Brain homogenates from LAG3 KO and WT mice were immunoblotted for the presence of murine LAG3. Western Blot does not show a specific band other than for activated murine T cells. B. Mixed neuroglial, neuron-enriched, and glial cortical cultures were assayed for the presence of LAG3 where no band could be found. Activated T cells display band at expected size. C. Lysates of synaptoneurosomes (SNS) of different brain regions and mouse brain region-specific areas as well as murine activated T cells were assayed for the presence of LAG3 with sandwich ELISA. No evidence for LAG3 could be found in any of the samples other than in activated T cells. Expression is shown in pg LAG3 per µg total protein as mean values of technical quadruplicates with 95% confidence intervals. D. Using high power, high resolution laser scanning confocal microscopy, no mouse LAG3 signal could be detected in murine primary neuronal cultures (Auto-mLAG3 transduced, DOX OFF and non-transduced neurons) using anti-mouse LAG3 antibody (MABF954) whereas LAG3 was clearly detected in primary neurons induced to express mLAG3 (Auto-mLAG3 transduced, DOX ON). Scale bars 20 µm. E. RT-qPCR-derived CT values to measure the cDNA copy number. Mixed neuroglial cultures, glial cultures, and neuron-enriched cultures show transcript levels that are close to indistinguishable to those from LAG3‑/‑ BH. Conversely, around 1600 transcripts/ng of RNA were counted in activated T cells. F. Murine mesencephalon and striatum of 1-year old mice (n = 17 in total) were interrogated with scRNAseq. Violin plot showing expression values of Lag3, in 76'305 assigned cells, between identified cell clusters, mainly expressed in TMEM119-positive microglia cells. Cluster markers are detailed in Russo et al. 2019.
Figure 3(A) Diagram of dosing regimen for the dose-dependent effect of MOTS-c on PMO activity in mdx mice. i.v. refers to intravenous injection. PMO-M (+MOTS-c) means PMO-M supplemented with additional MOTS-c. (B) Immunohistochemistry for dystrophin expression in body-wide muscles from mdx mice treated with PMO-M or PMO-M (+MOTS-c) (scale bar: 100 μm). TA refers to tibialis anterior. (C, D) Western blot (C) and quantitative analysis (D) for dystrophin expression in body-wide muscles from mdx mice treated with PMO-M or PMO-M (+MOTS-c) (n=3). 5 µg, 10 µg and 20 µg total protein from C57BL/6 and 50 µg of muscle samples from untreated and treated mdx mice were loaded. (E Immunohistochemistry of dystrophin-positive fibres in body-wide muscles from mdx mice treated with PMO at 12.5 mg/kg/week for 3 weeks mixed with MOTS-c (500 μg) (PMO-M) intravenously (scale bar: 100 μm) (n=3; *p<0.05). PMO represents PMO in saline. F) quantitative analysis of dystrophin-positive fibres in body-wide muscles from mdx mice treated with PMO at 12.5 mg/kg/week for 3 weeks mixed with MOTS-c (500 μg) (PMO-M) intravenously (scale bar: 100 μm) (n=3; *p<0.05). PMO represents PMO in saline. (G, H) Western blot (G) and quantitative analysis (H) of dystrophin expression in body-wide muscles from mdx mice treated with PMO at 12.5 mg/kg/week for 3 weeks mixed with MOTS-c (500 μg) intravenously (n=3; *p<0.05). 0.5 µg, 1 µg, 2.5 µg, 5 µg and 10 µg total protein from C57BL/6 and 50 µg of muscle samples from untreated and treated mdx mice were loaded. α-actinin was used as the loading control. Fold change refers to PMO-M relative to PMO alone.
Effect of liraglutide and RM-493 co-treatment on glucose metabolism in DIO mice.Figure 4A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (A) Fasted blood glucose levels. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered).(B, C) glucose tolerance. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (D) fasted insulin levels,. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (E, F) glucose-induced insulin secretion. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (G) HOMA-IR. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (H) insulin sensitivity. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001. A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (I) hepatic phosphorylation of AKT (p-AKTSer473) were analyzed. Compounds were administered by daily subcutaneous injections. To assess insulin-stimulated p-AKTSer473, insulin (n = 5) or saline (n = 3) was injected 10 min prior to liver sampling. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001.
a) Three GAL8 structures, including both CRDs, are available from PDB (4FQZ—lactose bound in only N-CRD; 3VKL—lactose bound in both N-CRD and C-CRD; 3VKM—sialylated lactose in N-CRD and lactose in C-CRD).f5(a) Three GAL8 structures, including both CRDs, are available from PDB (4FQZ-lactose bound in only N-CRD; 3VKL-lactose bound in both N-CRD and N-C-CRD; 3VKM-sialylated lactose in N-CRD and N-CRD in C-CRD). The C-CRDs of these Gal8 structures were superposed with that of our Gal8. For clarity, only Cα-traces of each structure (our GAL8-yellow; 4FQZ-red; 3VKM-blue; and 3VKL-cyan) are shown. The large rotation of the N-CRD domain relative to GAL8 compared with the other NDP52 structures is observed in the GAL8-NDP52 complex. A representative angle between CRD of our Gal8 and that of the 4FQZ structure is indicated in degrees. (b) A 90° rotation of panel (a) along the horizontal axis showing a top view. Arg59, which is a unique residue of Gal8CRD that provides carbohydrate specificity, is used as a standard for measuring the distance of domain movement.
Subunit topology of COMA.Figure 2A) Excerpt from a representative nanoflow mass-spectrum of COMA (full spectrum and enlarged spectrum areas are in Appendix Fig S2A); B) mass-spectrum from tandem mass-spectrometry of the isolated 28+ charge state of COMA (from spectrum shown in A), after its collision-induced dissociation in the gas phase. Charge states of assigned masses are indicated above peaks. For this spectrum and our other spectra of this type, charge states of assigned masses are indicated above peaks. Inset table shows identified proteins or protein assemblies, their measured mass values as mean ± standard deviation from multiple peaks in a peak series assigned to the same molecular species; and their respective expected mass.
Figure 4A. LukAB octamers (4TW1) highlighting the location of where the deleted residues would be in the pore structure (left- LukABmut1, right- LukABmut2), as shown from the side view of the pore. The octameric LukAB structure was obtained from the Protein Data Bank and the motifs labeled using PyMOL. B. Exoproteome analysis of LukAB mutants produced by S. aureus strain Newman in a toxinless background. Samples were electrophoresed on a 12% SDS-PAGE gel and visualized by staining with Coomassie blue. A representative of two experiments is shown. C. Exoproteome and immunoblot analyses of wildtype S. aureus strain Newman transformed with empty plasmid (p-) or with plasmids containing the mutated lukAB loci. A representative of two independent experiments is shown. D. Viability of primary human PMNs during a 2-hour ex vivo infection with the indicated S. aureus strains using the CytoTox-One Homogenous Membrane Integrity Assay to measure lactate dehydrogenase (LDH) release. Bars indicate Mean ± SEM, with n = 3. Statistical significance is indicated as follows: MOI of 100: **p = 0.0026 for p- vs LukABmut1 and ***p = 0.0003 for p- vs LukABmut2; MOI of 50: ****p <0.0001 for p- vs LukABmut1 and ****p <0.0001 for p- vs LukABmut2; MOI of 25: ***p = 0.0007 for p- vs LukABmut1 and ****p < 0.0001 for p- vs LukABmut2 using two-way ANOVA with Tukey's post hoc test correction for multiple comparisons.