EMBO/sd-character-level-ner huggingface dataset:
Figure 3(A-B) BMDMs were treated with PA, steric acid (SA), palmitoleic acid (PAO) or oleic acid (OA) (500 µM) for 16 hours. RNA lysates were analyzed by qRT-PCR for the expression of (A) miR-2137 and (B) sXBP1 (n=3 biological replicates). (C, D) (C) C57BL/6 (WT) and (D) Apoe-/- mice were fed with chow or WD for 16 weeks followed by peritoneal macrophage isolation. RNA lysates were analyzed by qRT-PCR for miR-2137 expression (WT; n=4-4 mice per group, Apoe-/-; n=5-5 mice per group). (E-F) Apoe-/- mice were fed with chow or WD for 12 weeks and injected with 4µ8c (10 mg/kg/day) or vehicle (DMSO) in the final 6 weeks of the diet (n=5-7 mice per group): (E) RNA lysates from bone marrow were analyzed by qRT-PCR for miR-2137 expression (n=5-7 mice per group). (F) Total RNA isolated from the aortic root plaques was analyzed by qRT-PCR for miR-2137 expression (n=5-7 mice per group).
Figure 1Representative IF staining of Sox2 (green) and Ki67 (red) on the P7 CLE stem cell and transit amplifying cell regions and counterstained with DAPI (blue) on a sagittal section. Dotted lines, basement membrane; yellow arrowheads mark approximate stem cell boundaries. SCs, stem cells; TACs, transit amplifying cells; Ant, Anterior; Post, Posterior. The mRNA expression profiling on specific markers of stem cells (B) and transit amplifying cells captured on P7 incisors CLE followed by analysis using real-time RT-PCR (C). qRT- PCR results are in arbitrary values after normalization for GapDH. Statistics was performed on triplicates using one-way ANOVA followed by Bonferroni's test. Representative IF double staining of E-Cadherin (ECad, green, for cell border) and AcTub (red, for the cores of primary cilia) on a sagittal section. Sample is counterstained with DAPI (blue). 3D reconstructions of ciliary cores of the stem cells and transit amplifying cells based on AcTub immunostaining. Quantification of cilia length (F) and volume (G) based on 3D reconstruction (E) and comparison between those in stem cell and transit amplifying cell regions. Numbers of quantified cilia were indicated (n). Statistics was performed using one-way ANOVA: All error bars were defined in Statistical Analysis section: All quantification and real-time RT-PCR results were presented using style of mean and standard deviation. Tamoxifen induced IFT88 deletion strategy (top panel) and representative images of Sox2 (green) and Ki67 (red) immunostaining on CLE regions of the indicated mouse strains (bottom panels). Dotted lines, basement membrane. Note the significant reduction of both Sox2 and Ki67 immunolabeling upon deletion of IFT88. 3D reconstruction of Sox2-positive regions based on its immunolabeling of the indicated mouse strains (I) and their volume comparison between mouse strains as indicated (J). Statistics was performed using Student's t-test: **, p < 0.01. Data are represented as mean and standard deviation. Representative IF double staining of ADP-ribosylation factor-like protein 13B (Arl13b, red, K) or histone deacetylase 6 (Hdac6, red, L) with AcTub (green) as a marker of the primary cilium core following stem cell to transit amplifying cell transition. Summary of the immunolabeling of Arl13b or Hdac6 with AcTub (K, L) along stem cell to transit amplifying cell transition.
Figure 1A Schematic illustration of the experiment. Clonal human brown and white adipocytes were subjected to RNA sequencing and mass spectrometry. B Bioinformatic analysis defined 16 secreted candidates (fold change ≥5) from brown compared to white adipocytes. C Schematic illustration of the experiment. C57Bl/6 mice (11 weeks old) received adenovirus (2x109 PFU/mouse) for each candidate via tail-vein. GFP adenovirus was used as a control. Seven days after adenovirus infection, mice were euthanized and inguinal (iWAT) and epididymal (eWAT) white fat were weighed. n=5 for all the candidates and control. D Changes (Δ g) in inguinal WAT (iWAT) mass of mice in (C). n=5. *P<0.05, **P<0.01 relative to GFP by Student's t-test. N.S., not significant. E Changes (Δ g) in epididymal WAT (eWAT) mass of mice in (C). n=5. *P<0.05, **P<0.01, ***P<0.001 relative to GFP by Student's t-test. N.S., not significant. F Expression of Pltp mRNA in indicated tissues. Data are shown by relative Pltp mRNA levels normalized by 18s expression. n=3 for all tissues (except BAT and WAT n=5, Testis n=2). *P<0.05 Pltp expression in BAT vs other tissues (except testis and lung) by Student's t-test. G Plasma PLTP activity from control (Ppargflox/flox) and BAT-less mice (Pparg UCP1-KO, Ucp1-Cre x Ppargflox/flox). Following 6-h fasting plasma was obtained from PpargUCP1-KO mice and littermate control. n=3 for both groups. *P < 0.05 relative to control mice by Student's t-test. H PLTP protein levels in the culture conditioned medium from primary differentiated inguinal adipocytes of wild type (WT) and aP2-PRDM16 mice [24]. Peptide levels was determined by quantitative proteomics. n=2 for both groups. I Transcriptional regulation of the Pltp gene by PRDM16 and PPARγ. ChIP-seq data for PRDM16 and PPARγ were obtained from [31,32], respectively.
Figure 5(A) Representative TEM pictures of HeLa wild-type cells. Bottom panels show healthy mitochondria. Scale bars, 500nm (overview) and 200 nm (zooms).(B) Representative TEM pictures of apoptotic HeLa wild-type cells 4h after STS treatment (1µM). Black arrowheads point to defects on the mitochondrial outer membrane. Scale bars, 500nm (overview) and 200 nm (zooms)(C) Representative TEM pictures of apoptotic HeLaGFP-Bax transfected cells 4h after STS treatment (1µM). Black arrowheads point to defects on the mitochondrial outer membrane. Scale bars, 500nm (overview) and 200 nm (zooms).
SCA8 BAC mice and human autopsy tissue show white matter abnormalities at sites of polySer accumulation A Disease-specific sensitivity to vacuolization after prolonged storage in ethanol shown by H&E in cerebellar white matter and brainstem of 10-12 month old end-stage SCA8 BAC mice but not in age matched NT (n=3) (panels 1&2).Figure 4A Disease-specific sensitivity to vacuolization after prolonged storage in ethanol shown by H&E in cerebellar white matter and brainstem of 10-12 month old end-stage SCA8 BAC mice but not in age matched NT (n=3) (panels 1&2). Demyelination shown by luxol fast blue staining (LFB) (panel 3) and axonal degeneration shown by α-SMI-32 (panel 4; degenerated axons are indicated by black arrows) observed in sites of polySer accumulation shown by α-SerCT (panel 5; representative aggregates are indicated by black arrows) in deep cerebellar white matter and brainstem in SCA8 BAC mice (lower panels) but not in NT mice (upper panels) (n=3).Demyelination shown by luxol fast blue staining (LFB) (panel 1) and axonal degeneration shown by α-SMI-32 (panel 2) observed sites of polySer accumulation shown by a-SerCT2 (panel 3) in deep cerebellar white matter was found in SCA8 autopsy tissue but not in control brains (n=3). C Immunohistochemistry using CC1 (α- APC) antibody shows significantly lower numbers of mature oligodendrocytes in SCA8 BAC mice compared to NT mice (NT n=5, SCA8 BAC n=5; **** p<0.0001; mean ± SEM; unpaired t test). D Immunofluorescence using α-GFAP antibody shows significant increase in astrogliosis in SCA8 BAC mice compared to NT mice (NT n=3, SCA8 BAC n=3, ** p<0.01; mean ± SEM; unpaired t test). E Cell death measured by lactase dehydrogenase (LDH) assay in T98 cells transfected with codon replacement constructs expressing polyGln (light blue) or polySer (dark blue). NT=nontransfected, EV=empty vector (n=5, ** p<0.003; *** p< 0.0003; mean ± SEM; unpaired t test).
Figure 7(A) HeLa cells were transfected with the indicated siRNAs. Seventy h after transfection, the lysates from the cells were subjected to immunoblot analysis using anti-TDP-43, DHC, DIC, Dynactin 1 and GAPDH antibodies. The relative densities are shown on the right side. Data from three independent experiments were represented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (B, C) HeLa cells were transfected with the indicated siRNAs. Seventy h after transfection, the cells were incubated with Earle's Balanced Salt Solution (starvation) for 2 h. Then the cells were stained with Lysotracker (red). Hoechst (blue) was used for nuclear staining. The stained cells were visualized using microscope IX71. Scale bar, 5 µm. The quantitative data of the localization of lysosome are shown in Figure 7C. Data from three independent experiments represented as means ± S.E.M., **, p<0.01, one-way ANOVA. (D, E) HeLa cells were transfected with the indicated siRNAs. Forty-eight h after transfection, the cells were re-transfected with LAMP1-RFP (red) for 24 h. And then the cells were incubated with Earle's Balanced Salt Solution (starvation) for 2 h. The cells were stained with anti-LC3 antibody (green) and DAPI (blue). Cells were visualized using a confocal microscopy. Regions within the dotted boxes are magnified in the insets. Scale bar, 5 µm. The quantification data of the colocalization of LC3 and LAMP1 is shown in Figure 7E. Data from three independent experiments represented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (F, G) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were transfected with LAMP1-RFP (red), with or without myc-Dynactin 1 for 30 h. And then the cells were incubated with Earle's Balanced Salt Solution (starvation) for 2 h. The cells were stained with anti-LC3 (green) antibody. Cells were visualized using microscope IX71. Regions within the dotted boxes are magnified in the insets. Scale bar, 5μm. The quantification data of the colocalization of LC3 and LAMP1 is shown in Figure 7G. Data from three independent experiments represented as means ± S.E.M., **, p<0.01, one-way ANOVA.
Figure 7 A. Representative confocal double immunofluorescence images displaying MBP (red) and NF200 (green) distribution and their coexpression (white) in the middle corpus callosum of septostriatal sections of control mice (a-c), and of mice fed with cuprizone for 5 weeks in the absence (d-f) or in the presence of D-Asp (g-i). Scale bars in a-i: 20 μm. (j), Densitometric analysis of MBP immunofluorescence signal and (k) quantification of MBP-NF200 colocalized points in the middle corpus callosum of septostriatal sections from control mice, and from mice fed with cuprizone for 5 weeks in the absence or in the presence of D-Asp Data information The values represent the means ± S.E.M. Level of significance was determined by using in: A, j, one-way ANOVA P<0.0001 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=4 mice for each group); A, k, one-way ANOVA P=0.0162 followed by Newman-Keuls post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=4 mice for each group  B. Western blot and densitometric analysis of MBP levels in corpus callosum lysates from control and cuprizone treated-mice for 5 weeks in the absence or in the presence of D-Asp, respectively. Data were normalized on the basis of α-tubulin and expressed as percentage of controls Data information The values represent the means ± S.E.M. Level of significance was determined by using i B, one-way ANOVA P<0.0001 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=3 mice for each group  C. Representative confocal double immunofluorescence images displaying GFAP (green) and Iba1 (red) distribution in the middle corpus callosum of septostriatal sections of control mice (a-c), and of mice fed with cuprizone for 5 weeks in the absence (d-f) or in the presence of D-Asp (g-i). Scale bars in a-i: 50 μm. (j-k) Quantification of GFAP+ and Iba1+ cells in the middle corpus callosum of septostriatal sections of control mice and of mice fed with cuprizone for 5 weeks in the absence or in the presence of D-Asp. Data were normalized to the total cell number (Hoechst signal) and expressed as percentage of controls Data information The values represent the means ± S.E.M. Level of significance was determined by using i C, j-k, one-way ANOVA P<0.0001 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=4 mice for each group  D. Western blot of GFAP and Iba1 protein levels in corpus callosum lysates obtained from control or cuprizone treated-mice for 5 weeks in the absence or in the presence of D-Asp, respectively Data information The values represent the means ± S.E.M. Level of significance was determined by using i D middle panel, one-way ANOVA P=0.0146 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=3 mice for each group); D right panel, one-way ANOVA P= 0.0026 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=3 mice for each group)
a) c-Cbl siRNA was transfected into FAK−/− cells expressing siRNA resistant, HA-tagged wild-type c-Cbl or c-Cbl mutants with defective E3 ligase activity (c-CblC381A or c-Cbl-70Z).figf8(a) c-Cbl siRNA was transfected into FAK−/− cells expressing siRNA resistant, HA-tagged wild-type c-Cbl or c-Cbl mutants with defective E3 ligase activity (c-CblC381A or c-Cbl-70Z). Left, cells were stained for anti-p-Tyr-416-Src (green), anti-HA (red) and with DAPI (blue). Solid arrows show co-localization in intracellular puncta. Scale bars, 20 μm. Right, quantification of percentage of cells that contained active Src in intracellular puncta. Data are presented as mean±s.d. and significance is P>0.5 (n=3). (b) Schematic illustration of the structure of c-Cbl and alignment of the potential LIR motif with those in known LC3B-interacting proteins. (c) GST-pulldown assay of HA-tagged wild-type c-Cbl, c-CblAA (W802A, L805A) and c-CblAAAA (W802A, L803A, S804A, L805A) expressed in HEK293T cells was carried out using GST-LC3. (d) c-Cbl siRNA was transfected into FAK−/− cells expressing siRNA-resistant HA-tagged wild-type c-Cbl or c-CblAAAA. Left, cells were stained for anti-pTyr-416-Src (green), anti-HA (red) and with DAPI (blue). Solid arrows indicate pTyr-416 localization to adhesions and dashed arrows indicate localization to intracellular puncta. Scale bars, 20 μm. Right, quantification of percentage of cells that contained active Src in intracellular puncta. Data are presented as mean±s.d. and significance is P0.01 (n=3). Uncropped images of blots are shown in Supplementary Fig. S9.
Figure 7SARS-CoV-2 induces a delayed inflammatory response that can be modified by specific pathway inhibitors. (Left) Infected lung epithelial cells sense SARS-CoV-2 RNA via cytoplasmic RNA sensors RIG-I and MDA5 to activate secretion of inflammatory mediators. Manipulation of RNA sensing early in infection by viral innate immune antagonists leads to a delayed and particularly inflammatory response. The infected cell secretome activates macrophages to potentiate an pro-inflammatory state at the site of infection. (Right) Inhibition of RNA sensing or downstream signalling pathways, for example with NF-κB inhibitors, reduces inflammation in infected cells and consequent activation of pro-inflammatory macrophages.
LINC00941 acts as a negative regulator of keratinocyte differentiation A qRT-PCR analysis of LINC00941 repression during keratinocyte differentiation in primary keratinocyte cultures from three different donors compared to undifferentiated keratinocytes (D0) (n = 6 biological replicates).Figure 1A qRT-PCR analysis of LINC00941 repression during keratinocyte differentiation in primary keratinocyte cultures from three different donors compared to undifferentiated keratinocytes (D0) (n = 6 biological replicates). Data is presented as mean ± SD. siPool mediated LINC00941 knockdown (B) in calcium-induced keratinocyte differentiation (n = 3 biological replicates/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value < 0.05, ** = adj. p-value < 0.01, *** = adj. p‑value < 0.001, and n.s. = not significant). siPool mediated LINC00941 knockdown in calcium-induced keratinocyte differentiation, results in increased abundance of early and late differentiation marker transcripts on day 3 of differentiation (C) (n = 3 biological replicates/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value < 0.05, ** = adj. p-value < 0.01, *** = adj. p‑value < 0.001, and n.s. = not significant). LINC00941 knockdown in day 3 (D3) organotypic epidermal tissue cultures (D) (n = 3-4 tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value < 0.05, ** = adj. p-value < 0.01, *** = adj. p‑value < 0.001, and n.s. = not significant). LINC00941 knockdown in day 3 (D3) organotypic epidermal tissue cultures results in increased expression of key differentiation genes (E) (n = 3-4 tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value < 0.05, ** = adj. p-value < 0.01, *** = adj. p‑value < 0.001, and n.s. = not significant). F Immunofluorescence analysis shows increased levels of early and late differentiation proteins. Collagen VII (col VII, green) stain indicates the basement membrane, nuclei are shown in blue and the differentiation proteins Keratin 10 and Loricrin are shown in red (n = 3-4 tissue cultures/knockdown group; one exemplary picture for each group is depicted). Scale bar: 50 µm.
svb is expressed in ISC/EBs and is required for their maintenanceA Schematic representation of the svb locus, showing location of enhancers as well as functional organization of somatic (Svb) and germline (OvoA, OvoB) protein isoforms.Figure 1Schematic representation of the svb locus, showing location of enhancers as well as functional organization of somatic (Svb) and germline (OvoA, OvoB) protein isoforms. Red and green boxes represent the repressor and activator domains, respectively; purple ovals depict the DNA-binding zinc fingers. The adult intestinal stem cell lineage, with markers of stem cells (Dl), enteroblasts (Su(H)) and enterocytes (Pdm1). Esg is expressed in progenitor cells gathering stem cells (ISC), enteroblasts (EB) and pre-enteroendocrines (preEE). Both pre-EEs and mature enteroendocrine cells (EE) express Prospero (pros). Posterior midgut showing expression of the E3N svb enhancer (GFP, green) in ISC/EBs, as shown by co-staining with esg-lacZ (β-Gal, red). ' Staining for Dl-lacZ (purple) or Su(H)-lacZ (red) in esgts midguts expressing GFP alone (control), or expressing svb-RNAi. Samples were stained for GFP (green) and ß-Gal. Closeups show separate channels for GFP and ß-Gal. The graphs show quantification of the number of ICS (Dl-positive) and EBs (Su(H)-positive). ' Staining for Dl-lacZ (purple) or Su(H)-lacZ (red) in esgts midguts expressing GFP alone (control), or expressing svb-RNAi. Samples were stained for GFP (green) and ß-Gal. Closeups show separate channels for GFP and ß-Gal. The graphs show quantification of the number of ICS (Dl-positive) and EBs (Su(H)-positive). Quantification of the number of YFP-positive cells (left) and GFP-positive cells (right) in control and upon expression of svb-RNAi driven by ISCts and Su(H)ts, respectively. Posterior midguts containing control or svbR9 MARCM clones (GFP, green), and quantification of the number of clones, and of the average number of cells per clone. esgtsF/O midguts expressing GFP alone (control) or expressing svb-RNAi. Samples were stained for GFP (green) and the apoptotic marker cleaved Dcp1(red). Arrows highlight GFP-positive cells that are also positive for Dcp1. Quantification of GFP-positive cells per posterior midgut in esgts expressing GFP alone (ctrl), or expressing DIAP1, svb-RNAi, and svb-RNAi+DIAP1.
Figure 4A. MLE-12 AECs co-incubated with the listed WT strains (MOI = 0.4) plus AM-EVs (grey bars, EV:cell = 1). Data represent mean M gene transcripts at 12 h post infection relative to the mean of the corresponding untreated strain (white bars), each normalized to β actin from 2-4 independent experiments per strain. B. Schematic flow diagram of the generation of luciferase-expressing patient-derived influenza viruses. The generation of the novel Luc-CA/09 strain is shown as a representative example. C. MHS EVs were co-incubated with the listed Luc-expressing strains plus AM-EVs (grey bars, EV:cell = 2) in MDCK-SIAT1 cells. Data represent mean luminescence AUC from individual wells normalized to the means of the corresponding untreated strain (white bars) from 3 independent experiments per strain.
Figure 8Figure 8. The working model of stromal cell-secreted Islr regulating intestinal epithelial Hippo signaling.
Fig.Figure 7(A) Immunofluorescence of the neuronal marker TUBB3 (red) in mouse motor neurons differentiated from mESC (mMN) or from NSC34 cells (NSC34DIFF) exposed to 2.5 μM (PR)20 for 24 and 48 hours, respectively, with or without 2 μM of a non-coding 38nt oligonucleotide. Nuclei were stained with DAPI (blue). Scale bar (white), 10 μm. Note that besides its impact on overall survival, the presence of the oligonucleotide also had a marked effect in rescuing neurite lengths that had been shortened by the peptide. (B,C) Cell viability quantified CellTiter-Glo luminescence assays mMN (B) and NSC34DIFF (C) treated as in (A) (n=3). Data represent mean values ± SEM. ( Data information: **, p<0.01; ***, p<0.001. (D) Immunofluorescence of the neuronal marker TUBB3 (red) in mouse motor neurons differentiated from mESC (mMN) or from NSC34 cells (NSC34DIFF) exposed to 2.5 μM (PR)20 for 24 and 48 hours, respectively, with or without heparin (0.5 μM). Nuclei were stained with DAPI (blue). Scale bar (white), 10 μm. (E, F) Cell viability quantified CellTiter-Glo luminescence assays mMN (E) and NSC34DIFF (F) treated as in (D) (n=3). Data represent mean values ± SEM. Data information: **, p<0.01; ***, p<0.001. S
Ref(2)P localization and expression in the adult brain of wild-type flies.Figure 1.(A) Confocal micrographs of adult brain of a young (2 d old) wild-type fly. Positive staining for Ref(2) P and ubiquitin is not evident. (B-D) Confocal micrographs of adult brain of an old (8 wk old) wild-type fly. Ref(2) P accumulates in protein aggregates that often colocalize with ubiquitin (arrows). The white rectangle in C indicates the area shown in D. (E and F) Western blot analysis of total cell lysates (E) and insoluble protein fraction (F) of wild-type young and old adult heads probed with anti-ref(2) P and anti-ubiquitin antibodies, demonstrating a significant increase in Ref(2) P and insoluble ubiquitinated protein levels in old flies.