EMBO/sd-character-level-ner huggingface dataset:
Blood glucose levels of intravenously (i.v.) injected wild-type mice at indicated hours post injection. 20 µg of purified serum IgG from cInsulin immunized mice (red, n=6) or CI mice (grey, n=5) was used for injection. Dots represent individual mice. Mean ± SD, statistical significance was calculated by using repeated measure ANOVA test, ***P < 0.001, ****P < 0.0001.
(B) Inhibition of autophagy blocks HMGB1 translocation. Cells were pretreated as indicated with 100 nM wortmannin or 10 µM Ly294002 for 1 h or ATG5-specific shRNA for 48 h and were stimulated with starvation (HBSS) for 3 h and immunostained with HMGB1- or LC3-specific antibody and Hoechst 33342. The mean nuclear/cytosolic HMGB1 intensity and LC3 punctae per cell were determined by imaging cytometric analysis. A representative Western blot of ATG5 level after shRNA and HMGB1 staining is depicted (right). In parallel, the indicated cells were transfected with GFP-LC3 plasmid and assayed for autophagy by quantifying the percentage of cells with GFP-LC3 punctae. *, P < 0.05, **, P < 0.005, and ***, P < 0.0005 versus HBSS group; n = 3. Ctrl, control.
Analysis of the early endosome marker EEA1 in fibroblasts transduced with control or VPS16-expressing lentivirus by confocal microscopy. (A) Representative confocal micrographs. Scale bar, 20 μm. (B) Quantification of EEA1-stained puncta number and intensities (ca 80 cells analyzed for each of n=3 biological replicates).
(B) The plating efficiency assay was performed with derivatives of BW25113 Δ8EDs pHV53(mepM) harboring the vector pHV7 or recombinant plasmids carrying each of the eight endopeptidase genes under the control of the ParaBAD promoter. In this assay, functional replacement of MepM is detected based on growth in media containing 0.2% or 1% L-arabinose for expression of the endopeptidase gene carried by vector pHV7, while by-passing the requirement for induction of the mepM copy of pHV53 by L-rhamnose. Complementation was observed with both concentrations of inducer for mepH, mepS, and pbpG. Overproduction of mepM encoded by the pHV7 derivative in the presence of the high dose of L-arabinose (1%) was lethal. The right panel presents the growth control performed in the presence of 0.2% L-rhamnose for induction of the mepM copy carried by pHV53.
HT-29 cells were treated as indicated. The release of IL-8 in cell culture media was analyzed by ELISA (H). Data are means ± SEM of four (H) independent experiments (***P<0.001, ****P<0.0001, ANOVA).
b, Exposure to 2DG or switch to glucose-free medium with or without glucose replenishment.
B, Hydrophobicity analysis of Apg9p based on the Kyte-Doolittle algorithm (Kyte and Doolittle 1982) predicts six to eight transmembrane domains.
A-D Effects of LAMTOR1 KD and ML-SI1 treatment on TBS-induced LTP (A) or LFS-induced LTD (C) in CA1. B, D Means ± SEM of fEPSPs measured 40 min after TBS (B, n = 4-5 slices from 4-5 mice) or LFS (D, n = 4-8 slices from 4-8 mice) in different groups. Data information: Slopes of fEPSPs were normalized to the average values recorded during the first 10 min baseline Statistical significance was assessed by two-way ANOVA with Tukey's post-test *P < 0.05, **P < 0.01, ***P < 0.001 compared with shSc P < 0.05, ##P < 0.01, ###P < 0.001 compared with shLAMTOR1. Insets show representative traces of evoked fEPSPs before and 40 min after TBS/LFS. Scale bar 0.5 mV/10 ms.
Mononuclear cells from bone marrow aspirates of newly diagnosed (#2, #5, #9 and #13) or relapsed (#7 and #12) MM patients were treated with mycolactone and/or BZ at the indicated concentrations, or vehicle as control, for 18 h. Then, MM cells were identified by staining with anti-CD38 and anti-CD138 antibodies A Following treatment, induction of apoptosis/necrosis was measured by exposure of annexin V and PI incorporation. Data are Mean % of live cells from technical duplicates, relative to controls.
C. Dihydroethidium (DHE) staining of optimum cutting temperature (OCT) covered tissues from the colons of WT and OMA1-/- mice; DAPI was used as counterstain. DHE was shown in red color, while DAPI in blue color (representative data from three independent experiments). D. Quantification of DHE staining. Error bars are presented as mean ± SD (n=3 biological replicates), statistical significance was assessed by a two-way ANOVA, **p < 0.01, ***P< 0.001.
PBMCs and plasma samples were collected from SARS-CoV-2 infected individuals at time of hospitalization (D1) and after 5 days (D5). E-J: Matched D1 and D5 plasma samples were available from 55 donors and protein levels were determined for IFNα2a (E, n=30), IL-3 (F, n=38), IL-8 (G, n=44), IL-6 (H, n=51), TNFα (I, n=42) and CXCL10 (J, n=46), note that some samples could not be quantified and were excluded from the analysis. Data information: Each dot represents a patient, lines with error bars show the median values with interquartile ranges Statistical significance was determined using the Wilcoxon matched pairs signed rank test *<p0.05, **<p0.01 ***<p0.001, ns= not significant.
(A) Schematic flowchart of LUAD cell in vivo metastasis model. QKI-5-overexpression and control vector A549 cells (3 × 106 cells/mouse) were i.v. injected into BALB/c nude mice (10 mice per group). TGF-β1 was injected i.p. at day 1, 6, 11, 16 after cell injection to achieve TGF-β-stimulated A549 cell metastasis.
Cartoon cross section of nematode body showing neurons, intestine, and hypodermis. Our data suggest a model in which neurons release biogenic amines like 5-HT into the body cavity as a neurohormone. Molecules of 5-HT bind receptors like SER-1, resulting in augmented transcription of P450 enzymes like CYP-34A4. It is possible that 5-HT and other biogenic amines signal to another regulatory layer of neurons, which in turn release peptide-based signals (not shown). CYP-34A4 converts n-6 PUFAs into n-6 eicosanoids, which are released from the ER and allowed to diffuse extracellularly. Released eicosanoids could act through receptors in the hypodermis, triggering changes in UPS activity in this tissue. This triangle of signaling affords multiple points of regulation to coordinate external environment, internal physiology, and UPS proteostasis.
B. MITOL prevents caspase-dependent cell death in mitophagy. WT or MITOL KO HeLa cells stably expressing HA-Parkin and HeLa cells were treated with DMSO or CCCP (10 µM) with or without Z-VAD-FMK (10 μM) for 24 h. Cells were stained with propidium iodide (PI) for counting fluorescence microscopy of the percentage of dead cells. Data represent the mean ± SD of three independent experiments (>100 individual cells were counted). For statistical analysis, a one-way ANOVA with Tukey post-test was performed, **P < 0.01. C. Cell death in mitophagy caused by MITOL deficiency depends on calcium leak. WT and MITOL KO HeLa cells stably expressing HA-Parkin or HeLa cells were treated with DMSO or CCCP (10 µM) with or without BAPTA-AM (10 μM) for 24 h. Cells were stained with propidium iodide (PI) for counting fluorescence microscopy of the percentage of dead cells. Data represent the mean ± SD of three independent experiments (>100 individual cells were counted). For statistical analysis, a one-way ANOVA with Tukey post-test was performed, **P < 0.01.
(B) Box-and-whisker plot showing quantification of mono-phosphorylated p-tau231 in control (n=10) and AD (n=10) TBS-soluble fractions using a targeted IP-MS method (P >0.05, non-significant, ns, Mann-Whitney U test).
Transmission electron micrographs of ATG2A/B DKO cells (upper left), DKO + ATG2A-WT (upper right), DKO+ ATG2A-mLIR (lower left) and DKO+ATG2A-mYFS( lower right) starved (EBSS) for 2 h. Clustered small vesicles (open arrowheads; DKO and DKO-mLIR) and autophagosomes (closed arrow heads, DKO+ATG2A-WT and -mYFS) indicated. Images are representative of n=3 independent experiments. Scale bars 500nm. ER= endoplasmic reticulum; N = Nucleus; Mt = Mitochondria; G = Golgi; AP = Autophagosome.
(F) The number of falls in the treadmill of WTFlx and Ndufs3 smKO male mice, starting at 2 months (n=8). Bars represent means ± standard error (SE). P values were calculated by Student's t test to determine the level of statistical difference. n.s.-not significant; *p<0.05, **p<0.01 and ***p<0.0001.
Physical appearance of wild type (WT), Wwox null (KO) or KO injected with AAV-hWWOX (2x1010) at P19.
(H-I) TEM images (H) and 2D profile (I) of pre-synaptic terminal sections contain SVs and mitochondria (m). Docked vesicles are indicated by a white arrowhead (H) and black circle (I) and are defined as a vesicle with its center located within 20 nm from the presynaptic membrane. Scale bar: 100 nm.
Assays performed as in B, but using a non-prenylated Rab1/Ypt1 substrate and in the absence of synthetic liposomes. Exchange activity with and without the Trs85 subunit are equivalent. Representative of n=3 independent experiments.
(B) Immunoblotting analysis of markers for stemness (SOX2, Nestin and Musashi-1) and differentiation (GFAP and TUJ1 (Neuron-specific class III beta-tubulin)) in GSCs in comparison with GSC-derived cells at different passage numbers (P1-P7).
Composite profile of Rrm3 occupancy across the average ORF plotted as Rrm3 percentage of significant ChIP hits per segment. Each gene was divided into 10 equivalent segments from the start and end coordinates (segments 2-10). Two additional segments of the same size were considered upstream (5′) and downstream (3′) of each ORF (segments 1 and 12, respectively). The average signal log2 ratio for Rrm3 significant hits that map on each segment was plotted.
(E) Representative contour plot from [Cx3cr1gfp/+ WT] BM chimeric mouse, verifying that infiltrating blood-derived macrophages (CX3CR1-GFP+) are indeed CD45hi, and showing that they are detectable only in retinas from eyes that underwent ONC, while absent in noninjured controls (red vs. blue line). Cells were pre-gated on CD11b. n = 3-4 per group.
Left: Representative immunofluorescent staining of α-tubulin in control and nocodazole (8 μM, 30 min) treated hRPEs. Scale bar: 20 μm. Right: Y FMI of control and nocodazole (8 μM, pre-treated for 10 min and incubated for the whole experiment) treated hRPEs moving on stiffness gradient gel.
(f,g) Immunofluorescence for endogenous Cx43 (green) in control NRK cells or those knocked down for Atg9 (g) maintained in the presence or absence of serum. E-cadherin staining (red) is shown to highlight PM in g and h.
Schematic representation of Svb maturation by proteasome processing, which is triggered by EcR-mediated expression of pri.
C ULK1+/+ and ULK1−/− cells were transfected with FUNDC1−Myc for 24 h and then harvested in the absence or presence of 50 nM bafilomycin A1 (BAF1). Cell lysates were immunoblotted.
(C) Effect of lactate on phosphorylated S6K (T389), 4E-BP1 (T37/46), ULK1 (S757) in COUP-TFII-silenced HCT116 cells.
MOG/CFA- but not CFA-injected mice contain reactive antibodies for retinal proteins in blood and show altered spatial visual behavior. (A) 7-9 days after injection, blood from MOG/CFA-injected (red) but not from CFA-injected mice (black), elicited strong antibody responses in ELISA. Antibodies for RIBEYE and SV2 were used as positive controls (green), secondary antibody only as a negative control (white). Normalized data are given as mean ± S.E.M. (N=4 (CFA); N=5 (MOG/CFA). ** p<0.01 (significance was assessed by Mann-Whitney test, precise p-values given in the figure)
(c,d) Histological analyses (haematoxylin and eosin staining) of lung tumours in KRas;Atg5fl/+ and KRas;Atg5fl/fl littermates 18 weeks after AdCre inhalation. (c) Nuclear and cellular polymorphy, more dense and sometimes irregular chromatin as well as more nucleoli in tumour cells of KRas;Atg5fl/+ mice as compared with KRas;Atg5fl/fl tumours. Sections were analysed 18 weeks after AdCre inhalation. Scale bars, 50 μm. (d) KRas;Atg5fl/fl tumours exhibited markedly increased apoptotic figures and necrotic areas in the centre of larger tumours (asterisk).
(A) Relative amount of miRNAs bound to HuR that are immunoprecipitated either from Fed or Starved Huh7 cells. Immunoprecipitated materials were separated into two equal halves to do western blot analysis of HuR and relative quantification of associated miR-122 and miR-21 were done by quantitative RT-PCR (mean +/- s.e.m., n=3). GFP used as negative control to confer the specificity of the anti-HuR3A2 antibody in immunoprecipitating HuR. The miR-122 content in the GFP-antibody immunoprecipitated materials was too low to get detected reliably using the qRT-PCR.
B Recovery phase-specific colocalization of CLK1 and SRSF9. HeLa cells were transfected with a FLAG-CLK1 expression vector, cultured for 16 h, and exposed to thermal stress (42°C for 2 h) followed by recovery (37°C for 1 h). FLAG-CLK1 and SRSF9 were co-stained using anti-FLAG and anti-SRSF9 antibodies, respectively, and the nuclei were stained with DAPI.
(F) Immunoblot analysis with pSox4 antibody of cell lysates extracted from E13.5 control and DKO forebrains. Red arrowheads indicate Sox4 phosphorylation band; red asterisks are non-specific bands. Numbers above blot are quantification of Sox4 phosphorylation levels normalized to total Sox4 and are expressed as fold change vs. controls (n=4 embryos, 3 litters).
A, B H3K18Ac IF in WT and SirT7-/- fibroblasts. Cells were pulsed with EdU (green), stained with antibody against H3K18Ac (magenta) and then counterstained with DAPI (blue). (A) Representative IF images of late S-phase nuclei (EdU positive; scale bar 5µm). (B) Quantitation of (A) throughout the cell cycle.
I. ELISA-mediated quantification of sTREM2 in conditioned media of human macrophages isolated from GRN-FTLD patients (n=3). sTREM2 could not be measured in conditioned media of human macrophages isolated from patient #3 due to low overall cell yield. Data points indicate individual patients. Data information: Data represent mean ± SEM. For statistical analysis of patient samples in comparison to HC, the unpaired, two-tailed student`s t-test was performed. Statistical significance was set at *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001; ns, not significant
E: Interaction dissociation constants between the different STARD3 FFAT peptides and the MSP domains of MOSPD2.
I, Depletion of PTPN3 attenuates TGF-β global gene responses. Venn diagram shows the number of differential expression genes (DEGs) with TGF-β treatment in control or PTPN3-depleted HaCaT cells by RNA-Seq analysis. The overlap represents TGF-β target genes that are commonly regulated in both cell lines. HaCaT cells transfected with siControl or siPTPN3 were harvested for RNA-Seq after treated with or without TGF-β (2 ng/mL, 8 h).
I Model depicting the survival program elicited by LDHA targeting that mounts resistance to LDHA inhibition in melanoma cells.
D,E Tethering assay with the indicated reporters containing a F-Luc(Leu)-V5 fusion in which all in-frame methionines were replaced with leucine. The corresponding western and northern blots are shown in Fig EV2K-N.F Schematic representation of the reporters used in panels (G,H).
Phosphopeptide peak intensity normalized to total TRF1 signal in samples containing only TRF1 plus bRAFWT or bRAFV600E
(F, G, H) Western blotting and densitometric analyses for LC3-II/LC3-I ratio and SQSTM1 protein levels in CTNSWT, CTNS-/-, and CTNSPatient cells cultured in the presence or in the absence of 25 nM BafA1 for 4 h, respectively (n = 3).
(A) During fasting, inhibition of Dab2-Akt association reduces the interaction of Akt with USP1-PHLPP1-TSC1 complex. Left: TSC1 was immunoprecipitated from the soluble fraction of muscles expressing shLacz or Dab2-DN from fed or fasted mice. Mouse IgG was used as a control for non-specific binding. Precipitates were analyzed by immunoblotting. Right: densitometric measurement of PHLPP1 and TSC1 blots, and data is presented as PHLPP1/TSC1 ratio.
Representative still images of control, Rod depleted cells and Rod depleted cells supplemented with RNAi resistant Venus-Rod treated with nocodazole and time in minutes indicated. Scale bar, 5 μm.
Overview of the systematic measurements using single-cell phenotypic and multiplex biochemical assays to profile signaling biochemistry and cell state in 10 BRAFV600E/D melanoma cell lines exposed to four RAF inhibitors and one MEK inhibitor at multiple doses and times. Multiplex single-cell immunofluorescence assays were used in the follow-up experiments on selected cell lines for treatments with vemurafenib, JNK-IN-8, and their combination.
Predicted amino acid sequence of the M. florum enolase (Mfl468). The PATRIC proteome comparison tool allowed the identification of orthologs in the four Mollicutes species for which a metabolic model was available, including the reactions to which they were associated in other models as well as their gene names and/or enzyme commission (EC) numbers. The Structural Systems Biology software (ssbio) was used to search for known protein domains in the amino acid sequence of proteins using the Protein Data Bank (PDB) as a reference. If any domain were detected, the I-TASSER suite was used to generate a tridimensional model of the protein, which was in turn used to obtain an EC number prediction with COFACTOR. Gold standard EC number identifications (yellow bar) were found using DETECT v2 which provides the likelihood of correct annotation (top). These predictions were compared to those from RefSeq, PATRIC, and COFACTOR (bottom). Sankey diagram presenting the sequential steps used to interrogate the 676 predicted coding sequences. The level of confidence specific to each approach was determined and is represented by the red (low) to blue (high) color gradient.
Structure-based amino acid alignment of Siz1 and Siz2 PINIT and SP-RING domains. Residues in Siz1 that make contacts within 4 Å of SUMO and E2 in the PCNA/Siz1/Ubc9~SUMO complex (pdb 5JNE) are indicated by cyan circles and magenta triangles, respectively. Contacts determined using the CCP4 program CONTACT (Winn et al, 2011).
(E) survival of mice was monitored over the indicated period of time and the significant of data was analyzed by log-rank test (P<0.0001); n=6 mice/group.
The number of sim-expressing nuclei as counted by automated spot detection over time (A) Continuous opto-Notch activation initially induces sim expression across a large number of nuclei. Over time, the majority of nuclei adapt to the input and terminate expression.
HepG2 cells, HAT1 KO HepG2 cells, and HAT1 KO HepG2 cells reconstituted with either wild type HAT1 or mutant HAT1 (T188A) were subcutaneously injected into athymic nude mice (N=6). The relative amounts of 3-PG and 2-PG were determined by ELISA assays in the tumor tissues. N = 6 biological replicates. Data are presented as mean ± SD. Student's t-test, **P < 0.01.
(J) Allele-specific expression ratios of X-linked genes are represented as heatmaps, with X-inactive genes in red (ratio ≤ 0.135), X-active genes in green (ratio > 0.135) and mono-allelic Xcas expression in blue (ratio between 0.5 and 1) (see colour code in (C) ). Genes are ordered by genomic position.
E. BAZ2A is expressed at similar levels in both ESC+2i and ESC+serum. Left panel. BAZ2A mRNA levels were measured by qRT-PCR and normalized to Rps12 mRNA and to ESC+2i. Average values of three independent experiments. Error bars represent s.d. Right panel. Western blot showing BAZ2A protein levels in ESC+2i and ESC+serum. Tubulin and histone H3 are shown as a protein loading controls.
Average rootstock/scion ratio of amiRSUL levels as measured in (C), Fig.1G, Appendix Fig.S3A and Fig.S12B. Error-bars: SD. t-test p-values are indicated. n≥4.
(a-b) eIF4A knockdown in either S2 (a) or Kc167 (b) cells blunts the inactivation of TORC1 upon amino acid removal. Cells were treated with dsRNA targeting GFP as a negative control, or three independent, non-overlapping dsRNAs targeting eIF4A for 5 days and then incubated with complete medium or medium lacking only amino acids for 30 minutes. Representative of 3 biological replicates.
(B) Final level of mitotic regulators and Cdk1-substrates in response to cyclin synthesis. The heat map is based on model simulations starting with initial conditions without cyclins (Interphase, top row) until high and constant cyclin levels caused by APC/C inhibition.
(M) The apoptosis levels between WT and KO brains showed no significant difference. E16.5 brain sections of WT and KO mice were subjected to TUNEL assay. Scale bar represents 50 μm. (N) Graph shows the numbers of apoptotic cells per field. n=4mice, independent replicates. Date information: Representative images from at least three independent experiments. Error bars represent the means ± S.E.M.; Two-tailed unpaired t-test, P < 0.05(*). n.s., not significant.
Quantification of Tip30 and eEF1A1 mRNA transcript abundance in human failing hearts (A), N=6 to 8 hearts/group A ratio of Tip30 and eEF1A1 expression was calculated
B, C Cranial MRI analysis (B) shows the drastically enlarged ventricular cavity (marked by V) and diminished cerebral cortex tissue, (C) also seen when brains are cut in coronal orientation.
(A) Fluorescence microscopy of GFP-Atg8p expressing wild-type (WT) and ACH1-deleted (Δach1) yeast grown to day 1 (young) and aged for 3 days in SC 2% glucose medium; propidium iodide (PI) counterstaining served to visualize dead cells. Scale bars represent 5 μm.(B) Quantification of cells depicted in (A) with 150-300 counts (blinded) for each replicate. Autophagic cells were defined as cells with clear vacuolar GFP fluorescence. Data represent means ± SEM (n = 4). ∗∗∗p < 0.001.(C) Representative immunoblot analysis of cells shown in (A) and further aged to day 5 using anti-GFP and anti-GAPDH (loading control) antibodies to detect "free-GFP" indicative of autophagic flux (see also Figure S2).
(D) C3 surface levels at the surface of HIV-1-infected primary CD4 T cells. Results are expressed as MFI of staining on infected (Gag+) cells. Each dot represents a single donor of CD4 T cells. n=7 donors of CD4 T cells. Data information: Error bars indicate SEM. *P<0.05, **P<0.01, Wilcoxon test. Only significant comparisons are depicted.
D The early flowering phenotype of sec-5 mutant under long-day (LD) conditions. Scale bar: 1 cm.
A-B. Co-IP assays of endogenous proteins of GASZ and MFNs from adult testes (B).
(c,d) Molecular dynamics simulations of TREM2-TMH wt (c) and K186A (d) in a POPC/POPG (3:1) bilayer provide information on the stability of helix insertion into a lipid bilayer membrane. Since K186 is initially located in the hydrophobic membrane, its positively charged side chain is pulled towards the negatively charged phosphates in the lipid head group region leading to a pronounced tilt in helix orientation in the nanosecond time scale and on a µ-second to milli-second time scale to a kink in the C-terminal half of the α-helix, as probed by NMR line broadening. In contrast, in the K186A variant the transmembrane helix is stably inserted within the bilayer.
(a) Knockdown of p62 expression attenuates the LC3-Dvl2 interaction. shRNA, short hairpin RNA.
I. Wnt inhibition potentiates DNA double strand breaks induced by olaparib treatment. (I) Representative immunofluorescence images of 53BP1 foci (red) and nuclei counterstained with DAPI (blue) are shown for each group.
A. Representative immunofluorescence images of the association of MavQ with the LCV. BMDM cells infected with wild-type or Dot/Icm-deficient (dotA-) L. pneumophila were sequentially stained with antibodies against L. pneumophila and MavQ. Images were taken under a fluorescence microscope. Insets represent 3x magnification of regions defined by dash lines. Scale bar, 5 μm.
(D) Staining for Sox2 in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm. (E) Graph shows the number of Sox2+ cells in 4x104 μm2 in enlarged SVZ (WT n=3; hFOXM1-cKI n=4; two-tailed unpaired t-test, P=0.0292). (
a) Autophagy induction in response to 5-FU measured in a GFP::LGG-1 reporter strain fed control RNAi (L4440) or RNAi targeting the indicated genes (scale bars, 10 μm).
B Quantification of total cellular PI3P levels in sh-Control or sh-PI3KC2β hCMEC/D3 cells by mass assay. Results are expressed as pmoles of PI3P/nmoles of total phosphore. Data represent mean ± SD (n=2 independent experiments in triplicate).