EMBO/sd-character-level-ner huggingface dataset:
(J) Representative brightfield images for secondary organoid formation pretreated with DMSO or 10 nM TCDD for 2d. Scale 200 µm.
D) Log2 Fold Change (log2FC) of RNA-seq between female (F) and male (M) embryos of X- chromosomal genes which are constitutively (left, total=303) or developmentally expressed (right, total=303) in 7 developmental stages. P-values (pval) are calculated by one-sample Wilcoxon signed rank test to assess the median log2FC values against zero (balanced expression); ns: non-significant (p-value > 0.001).
B) The nucleus is progressively deformed over time in culture. For each time point, equatorial Z stacks of two representative cells are presented. Left panel: inverted image of chromatin (DAPI). Right panel: microtubules are shown in green and chromatin in blue. Scale bar: 5 µm. C) Nucleus volume (left panel) and invagination ratio (right panel) increase to attain levels similar to those of freshly isolated CD33+ cells (24 h, n=165, 4 donors; 48 h, n=143, 3 donors; and 72h, n=192, 4donors; CD33+, n=227, 5 donors; Bars correspond to mean ± SD; n.s: non significant; ***: p<0.001, ****: p<0.0001; Mann Whitney test).
(J) Bar graph representing the normalized average value of synaptic ATP level on the basal condition, on DHPG treatment for 5 minutes, on DHPG treatment with MPEP, on DHPG treatment with anisomycin and on DHPG treatment with cycloheximide (350μM). Data presented as mean ± SEM with scattered data points. Values in all other groups were normalized to the basal group for the corresponding experiment. *p<0.05, n=8 animals.
Analysis RAB2A expression was performed on the Invasive Breast Cancer Consecutive Cohort (n = 622) operated in the European Institute of Oncology, Milano, Italy, in the year 2000. Expression was measured by IHC on TMA.(c) Kaplan-Meier Distant Recurrence Free Interval survival (DRFI [70]) and (d) Univariate and Multivariate Cox-regression analysis, shows that in BC patients' high levels of RAB2A protein predict a poor prognosis, and that RAB2A expression is an independent predictor of higher risk of developing a distant metastatic recurrence.
Figure 7. Model for the regulation of Notch target genes by L3MBTL3. A NOTCH ICD binds to RBPJ-bound Notch-responsive elements where it builds up a coactivator complex composed of Mastermind-like 1 (MAML1) and additional co-activators to induce expression of Notch target genes. B In the absence of Notch signaling, L3MBTL3 interacts with RBPJ at Notch-responsive elements where it recruits KDM1A to repress Notch target genes. C Loss-of-function of L3MBTL3 leads to de-repression of Notch target genes.
Left - Scheme for identifying sites that lose 5hmC and their association with POU5F1 binding. Right - Heatmap of 5hmC profile during AA+2i treatment of WT pre-iPSC and POU5F1 binding in pre-iPSCs or mESCs at the loci identified in the left panel.
(i) In solid phase transfection, the microwell plates are coated with the transfection mixes consisting of synthetic gRNAs, lipid reagent, sucrose and gelatin. The microwell plates are then freeze dried and can either be stored for long periods of time or (ii) the cells can directly be seeded on these pre-coated plates. Wide range of readouts such as microscopy, flow cytometry or cell viability assays are possible.
E. A mutant tau that does not bind Hsc70 is not released when FLAG-DnaJC5 is overexpressed in HEK293T cells. Dot blot and quantification of extracellular tau levels are shown. Intracellular protein levels are shown with representative Western blot, DnaJC5 was detected by FLAG antibody. Data are mean ± SEM, n=3 p<0.001. one-way analysis of variance with Tukey's multiple comparison post-hoc analysis.
(F) From the seven tumors, the top hundred genes (enriched) have been selected and common genes are SMAD3, BIRC3 and SLC9A5
F. The decrease in MCH mRNA levels observed 18h after icv CCL2 injection is abolished by the CCR2 antagonist INCB3344 (10μM) and in CCR2 KO mice, as shown by real-time PCR analysis for MCH in the hypothalamus. Results were normalized to values in icv saline injected WT mice (n=6 per group). Data are expressed as means ± SEM. ** or $$ p<0.01. * saline vs icv CCL2 injection in WT mice. $ icv CCL2 injection in WT mice vs CCL2+INCB3344 icv injection in WT mice or icv CCL2 injection in CCR2 KO mice.
(C) Schematic diagram of full-length RDH/CG2064 and TM domain-deleted RDH/CG2064 (∆TM). Lysates of Drosophila S2 cells expressing the different proteins were immunoprecipitated with anti-GFP antibody and detected by anti-GFP or anti-Flag antibody in a western blot. Both full-length and ∆TM RDH/CG2064 were coimmunoprecipitated with Plin2.
Zinc, ifenprodil and pH dose-response curves of wild-type (WT) GluN1/GluN2B receptors and mutant GluN1-E698C/GluN2B-L795C receptors. For comparison, zinc and ifenprodil dose-response curves of GluN1/GluN2B receptors lacking the whole GluN2B NTD (GluN1 WT/GluN2B-delNTD) are also shown (dashed lines; data from Rachline et al, 2005)
Quantification of donor cells' contribution in E7.5 embryos, data represent mean ± SD, Ronin fl/del n embryos = 14, Ronin del/del n embryos = 8.
(E) Representative sections of spinal cords from tadpoles injected with EdU at 3 dpa and fixed at 5 dpa. After sectioning, the samples were labelled with antibodies against Myt1 (green), EdU (magenta) and DAPI (blue). (F) Quantification of images shown in (E). The graph represents the mean +/- SD from 3 tadpoles with an average of 12 sections each.
C. ChIP assay from IL-6 stimulated or non-stimulated 22Rv1 cells with or without knockdown of STAT3 was immunoprecipitated with a STAT3 specific antibody (blue shades) and IgG antibody as negative control (orange shades) followed by qPCR with a promoter- specific primer pair for the PDK4 gene. Bars represent mean ± SD from 2 technical replicates. Precipitated DNA is presented as % of input. One representative experiment is shown. Result of qPCR using primer pair 2 is shown. Ctrl = scrambled control, shSTAT3 = short hairpin knockdown of STAT3, +IL-6 = IL-6 stimulated.
Effects of the deletion of APG5 or APG7 on Apg12p-Apg10p thioester formation. Coimmunoprecipitation was performed with wild‐type (KA311B), Δapg5 (YNM122) or Δapg7 (YTS12) cells harboring HAAPG10 and MycAPG12 on 2μ plasmids. The resulting precipitates were analyzed by Western blotting. The DTT‐resistant Apg12p-Apg5p conjugate is indicated by ●.
A. Dose-response relationship between icv LPS injection and mice weight loss (n=6 to 12). Data are expressed as means ± SEM. *p<0.05, **p<0.01, ***p<0.001, color-coded asterisks indicate a significant difference from the experimental condition assigned to the respective color-coded curve.
b, p62 immunoblot of brains of 5-day-old GFP-LC3 mice treated with the indicated peptide (20 mg kg−1 i.p., 6 h).
Mouse YUMM1.7 melanoma cells were subcutaneously inoculated into C57BL/6 mice and when tumors reached 100 mm3 mice were treated with vehicle (Ctrl), Nintedanib/BIBF1120 (BIBF), MAPKi (BRAFi, Vemurafenib and MEKi, Trametinib) or BRAFi/MEKi plus BIBF (n=6). (G) Heatmap showing the differential expression of ECM and myofibroblast/CAF genes in mice treated with MAPK-targeted therapies with or without BIBF compared to control mice (log2 ratio, n = 5).
C. Metabolic pathways depicting the synthesis of PC and PE in P. falciparum. PMT and EK, which are putative targets of PfCDPK7, are indicated in red
E. Acetylated tubulin staining in 28 hpf controls (left) and mutants (right) showing severely affected outbranching of the trigeminal nerve (Vth cranial nerve). Notably, chd7-/- display reduced branching of the Vth cranial nerve (arrows) and axonal arborisation in the tectal area. Graphs showing quantitative analyses of percentage (n=5) and mean total length of peripheral projections (n=6) per zebrafish in controls and mutants (***p<0.001; **p<0.005, Student's t-test).
(g) Quantification of tumor volumes day 6 RasV12; ctrl (n=7), RasV12; scrib-/- (n=11) and day 8 RasV12; scrib-/- (n=13), RasV12, scrib-/-, atg13-/-//atg13-/- (n=9) and ey3.5-atg13; RasV12, scrib-/-, atg13-/-//atg13-/- (n=9).
D) H3K9me3 loss from the nucleus periphery occurs locally in nuclear invaginations. Line scans of H3K9me3 signal along nucleus contour of 2 representative cells are presented in the upper panel for each time point. Asterisks indicate the local loss of H3K9me3. The corresponding variations in H3K9Me3 intensity and curvature are plotted in blue in red, respectively. Negative curvature values correspond to local nuclear invaginations.
A to F Mice were vaccinated three times with AAV-vectors or two times with WIV and then challenged with a lethal dose of homologous influenza virus (Cal/7/9) (A, B; n = 5) or two different lethal doses of the heterologous PR8 strain (C, D; n = 6 and E, F; n = 7). Survival was monitored over a 14-day period and is depicted as Kaplan-Meier plot (A, C, E). Weight loss was determined during the 14-day period, which is shown in relation to the weight at day 0 (B, D, F). Mean ± SE. Statistical significance between negative control group (AAV-GFP) or WIV group (E) and each vaccine group was determined using Log-Rank (Mantel-Cox) test (*p<0.05, **p<0.01).
(F-G) Expression of Hif1α was modulated with overexpression or sh-RNA-mediated knockdown via a retrovirus system during reprogramming (F). The numbers of Oct4GFP+ colonies were determined on day 15 (G).
K. 49 compounds that improved motility phenotypes in chd-7(gk290) mutants were identified. These compounds were clustered in 6 main functional categories.
(E and F) Immunoblotting analysis for GLUT1 protein expression in control and MIG-6 knockdown BT549 (E) and MDA-MB-231 (F) cells with or without GLUT1 overexpression.
Chyle phenotypes in P7 Foxp2flox/-;Tie2-Cre and littermate controls (n = number of mice as indicated).
Pearson's correlation analysis showed that a significant negative correlation between the level of ASS1 and LOC113230 in CRC samples. R2=-0.53. P < 0.05. The LOC113230 and ASS1 expression levels were normalized to the GAPDH level, respectively.
A) ATP content in ES (blue), Zscan4+ (red) and 2-cell-like cells (green) across 4 independent biological replicates.
(j) Pearsons correlation coefficient of mean nuclear Venus::HES5 intensity with distance after subtraction of radial gradient in Venus::HES5 intensity; red dots represent average in each of 12 slices from 3 experiments.
A, B Expression and localization of Rny1 and Pho8. Wild‐type cells and atg2∆ cells expressing Rny1‐GFP or Pho8‐GFP were grown in SD to mid‐log phase and transferred to SD(‐N). After 2 h of starvation, GFP‐tagged proteins were analyzed by Western blot with anti‐GFP antibody (B).
(C) Effects of NAT on corticosterone concentrations in the serum of mice (Slc:ddY, 9-10 wks old, male) exposed to restraint stress for 60 min (data are means ± SEM; n=6). ** P<0.01 vs. without stress. Test mice drank 1.5 mg/ml NAT solution for 24 h before exposure to stress.
E As in (C) except HEK293 cells were transfected with the indicated N‐terminal Znf‐UBP domain‐containing DUBs. Similar results were obtained in at least two separate experiments.
a, Percentage of cells with small htt103Q aggregates (left) and number of aggregates per cell (right) in HeLa cells expressing doxycycline (Dox)-repressible CFP-htt103Q after daily treatment with doxycycline or peptide (20 μM, 4 h per day) for 2 days. Bars represent mean ± s.e.m. of triplicate samples (60-120 cells per sample). Similar results were observed in three independent experiments.
(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).
B-E. Study of gene and protein hypothalamic expression of MCH peptide (D, E) in icv CCL2 injected mice. Measurement of MCH (E) concentration by EIA after icv CCL2 injection (black bars) or icv saline injection (grey bars) in mice at 1h, 6h and 18h after injection. Cerebellum was used as negative control (3 independent experiments, n=6 per group in each experiment).
E Tyrosine phosphatase activity in anti-IDO1 immunoprecipitates from lysates of P1.HTR transfectants as in D.
A. Localization of TRAPP complex components after sodium arsenite (SA) treatment in HeLa cells treated with 300 µM SA for 30 min. Fluorescence microscopy of fixed cells using antibodies against TRAPPC2 and eIF3 (to label SGs) at steady state and after SA treatment (top two rows). Other panels show localization of GFP-TRAPPC3 and endogenous TRAPPC1 to eIF3-labeled SGs and of endogenous TRAPPC9 and TRAPPC8 to G3BP-labeled SGs. DAPI (blue). Scale bar, 10 µm.
Relationship between area and polygon distribution. A) Area distribution of several Voronoi diagrams along the CVT path. Cell areas became progressively more homogeneous after each Lloyd iteration
Graphs showing the changes in the fura-2 ratio in cells of the indicated genotypes in response to GPN. the baseline ratios for both genotypes were adjusted to 0 at the start of the experiment. Lines on the right indicate peak amplitudes of Ca2+ release Ca2+ release was evoked using GPN.
Immunoblot of phosphorylated JNK (p-JNK), JNK, phosphorylated c-Jun (p-c-Jun) and c-Jun in oncospheres from SUM159-LM1 cells. Tubulin was included as a loading control.
(C) Fusion triggers fission. Cumulative probability of the occurrence of fission events at different intervals after fusion events occur (fraction of all fission events occurring after the given time interval). The data are fit to a hyperbolic function representing linkage between the two events (INS1, R2=0.98; COS7, R2=0.96). The straight line shows the predicted linear growth rate in fission event probability over time that would be expected if the fission had occurred independently from the fusion events (dashed lines INS1, R2=0.77; COS7, R2=0.84; see Supplementary data).
Whole brain weights of 9-month-old animals revealed pronounced brain matter loss in rTg4510 compared to WT mice (weight loss >16%), which was rescued in rTg4510-Mapt0/0 mice to >96%. Mean±SEM, n=5 mice/group.
(D) Calcium accumulation in mitochondria after 24 h of incubation in MEM media containing 10 µCi/mL calcium-45 (45Ca2+) as a radiotracer.
F, G. The overlapped genes between the maturation-directed decay genes and the upregulated (F) or downregulated (G) genes in U0126-treated MII oocytes. FC, fold change.
H. Endogenous levels of Stim1 in testes from C57BL/6 wt and splice deficient 10A mice, using an antibody detecting the N-term of STIM1, detecting STIM1A (A, red arrow), STIM1 and its glycosylated (wt) and unglycosylated (wt gl.) form.
I. WB analysis of HCT116/L-OHP and SW480/L-OHP cells transfected with either HA-lnc-AP OE plasmid.
B: Data represent the mean and standard deviations of mCherry-Securin fluorescence intensity in WT and Cnot6l-/- oocytes at each time point. Values from individual oocytes are normalized relative to that at 0 h after released from GV arrest. The numbers of analyzed oocytes were indicated (n)
F The global RNA m6A level in sorafenib-resistant HepG-2 cells with wild type METTL3-overexpression or catalytic mutant METTL3-overexpression by dot-blotting assay.
Neurons expressing M18Y473D are not impaired at SV docking. Autaptic munc18-1 null hippocampal neurons expressing M18Y473D or M18WT as controls were analysed with electron microscopy on cryofixed samples (H) Total number of SVs is similar (M18WT: 160.2 ± 9.7 SVs; M18Y473D: 176.7 ± 9.2 SVs, multilevel analysis, p = 0.212).(G-J) M18WT : N=3 independent cultures, n=159 synapses; M18Y473D: N=3 independent cultures, n=156 synapses.
Proliferation inhibition analysis of ara-C and RNRi combination treatment in SAMHD1+/+ or -/- THP-1 cells. Error bars indicate s.e.m. of two (HU and dF-dC) or three (3-AP) independent experiments, each performed in duplicate.
B) Energetic landscape of the model in (A). Acidic GKs are indicated in red, basic GKs in blue and the non-gatekeeped energy landscape in grey. GKs thermodynamically destabilize and kinetically slow down the folding reaction, resulting in higher energies for N and TN⇋U. Acidic residues have a similar effect on the aggregated state, decreasing aggregate formation kinetics and thermodynamic stability. Basic residues on the other hand, only marginally affect aggregate stability and mostly work through deceleration of the aggregation process through an increase in TU⇋A energy. Through specifically binding positive residues, Hsp70 slows aggregate formation kinetics for positively gatekeeped APRs. Hence, Hsp70 increases GK potential of basic residues, preventing aggregation and allowing for a stable native fold.
Identification of LRPPRC as a novel ASS1 interacting protein. Cell extracts prepared from SW-1116 cells expressing Flag-ASS1, Flag-ASS1/LOC113230 300-800 or empty vector were incubated with M2 beads and the co-eluted proteins were resolved on SDS-PAGE gel and detected by silver staining assays. The specific band was collected and the potential proteins were identified by Mass spectrometry.
C. Human protein kinases phosphorylate large sets of yeast proteins. Upper panel: In total, 27 human protein kinases showed activity towards yeast proteins visible on western blots through enhanced reactivity with phospho-motif antibodies on yeast proteins in comparison to other human kinases, kinase‑dead mutant versions or vector control samples. Commercially available pS/T-antibodies with relatively low sequence specificities were chosen to enable detection of phosphorylation of the yeast proteome by human kinases. Lower panel: Examples of western blots with equal amount of whole yeast cell lysate from strains expressing human kinases loaded. When developed with the indicated phospho-motif recognizing antibodies, immunoreactive bands indicated phosphorylation of yeast proteins.
(B) Recruitment of Stx6-positive vesicles to rBCVs (expressed as percentage of Stx6-positive BCVs) in BMMs infected for 24 h with either wild type (2308), ∆bspF or complemented ∆bspF (∆bspF::bspF) bacteria. Data are means ± SD from n=3 independent experiments, in which at least 300 BCVs were analyzed per experiment via CellProfiler image analysis. Asterisks indicate statistically significant differences compared to 2308-infected BMMs as determined by one-way ANOVA with Tukey's multiple comparisons test (P < 0.05).
Schematic diagrams of RIα regions subjected to in vitro binding assays. Results from the RIα-SPATC1L interaction assay (Fig. 3B) are indicated as + or - at right. D/D, dimerization/docking domain (binding site for AKAPs); Domain A, catalytic subunit binding domain and cAMP binding domain; Domain B, cAMP binding domain; IS, inhibitor sequence (binding site for the active site of the catalytic subunit).
Western blot results showing that knockdown of endogenous E6 in HeLa cells with HPV18E6 siRNA (siE6) reduced YAP protein levels, but increased SOCS6 protein levels.
(c-f) Heart-to-body-weight ratios (c) in Sham-operated WT mice and miR-212/132 null and WT mice3 weeks after TAC surgery (n=4-7). Scale bar, 50 μm.
(C) Immunoblot analysis of the level of P‐ACC and GAPDH (loading control) in lysates from MCF10A cells treated with 500 ng/ml TRAIL for the indicated times.
C. Relative extent of MT lattice decoration based on average intensities of layer lines representing NDC (8 nm periodicity) and tubulin (4 nm periodicity) in averaged Fourier transforms of WT-MT and NN-MT segments, as described in Appendix Fig S6 and in Materials and Methods.
(B) Voltage dependence of the WT ClC-5 off-gating charge normalized to the ionic current at +165 mV in the absence or presence of adenine nucleotides (n=7-12). Error bars represent SEM. Red lines depict Boltzmann fits to the data; fit parameters are provided in Appendix Table S1.
(A) Mitochondrial extracts from 143B cells, COX1∆ and COX2∆ mutant cybrids and their respective isogenic controls (CON-1 and CON-2) were analyzed by SDS-PAGE and immunoblotting with the indicated antibodies. The graphs (right) show densitometric quantifications of the signals normalized to CII subunit SDHA. The mean of three independent controls (CON) was set to 100 and all measurements were referenced to that value. The values represent mean ± SD (n=3-8). Mann-Whitney U test was applied for statistical analyses. Variations between controls and mutants: α, p<0.05; β, p<0.01; γ, p<0.001. Specific variations between COX1∆ and COX2∆ mutants: ∗p<0.05; ∗∗p<0.01.
12 month old Ptpn2fl/fl;p53+/- and Lck-Cre;Ptpn2fl/f;p53+/- mice were assessed for a) disease and tumour incidence.
(F, top) Brightfield images of Rbf/f myoblasts transduced with Ad.EV or Ad.Cre and induced to differentiate under hypoxia. (bottom) Larger view of the boxed field. Arrowheads point to rescued Rb−/− myotubes. This field is shown in Video 6.
Ecto-5′-nucleotidase activity measured in membrane protein preparations of Arabidopsis plants expressing Pro35S::E5′NT (#303), Pro35S::SPE5′NT:mCherry:E5′NTwoSP (#304) or Pro35S::mCherry (#305). E5′NT activity was measured after incubation with 100 µM of either ATP, ADP or AMP. In the membrane protein preparations from Pro35S::E5′NT (#303) lines phosphate release was specifically increased upon incubation with purines. Error bars represent the standard error of the mean from three technical repetitions. The coomassie stained SDS-PAGE shows the protein pattern of the membrane fractions for the individual transgenic lines. Equal volumes were loaded. The experiment was repeated two times with similar results.
(B) Immunoblotting of whole cell lysates immunoblotted following treatment with antimycin A and oligomycin (AO) for 3 h with MG132 (20 µM). Graph shows densitometric analysis of non-ubiquitinated proteins relative to untreated control from three independent experiments. Error bars represent mean +/- SD.
(B) WT and SKO cells were treated with OA for 20 h, fixed and stained with LD540. Maximum projections of deconvolved confocal z-stacks. Dashed lines indicate cell boundaries. (C) Analysis of LD areas of cells treated as in (A) and imaged with widefield microscopy. Bars: % of LDs/field of view in indicated size category, mean ± SEM, n=25-30 fields of view (100-120 ROIs of not clustered LD areas from 100-120 cells), 2 experiments, p**< 0.005 (unpaired T-test). See also Appendix Figure S5D.
(B) Representative of three Western Blot analysis of endogenous p150Glued, light-intermediate chain (LIC) of cytoplasmic dynein 1 and EB1 immunoprecipitated with STIM1 in wild-type ECs. Negative control (CTL) was performed incubating cell lysate with protein A- or G-Sepharose and empty rabbit IgG.
B Lentiviral knock‐down/re‐expression constructs for THEMIS‐wt‐Strep and THEMIS‐dPRR1‐Strep in 1G4‐CD8 cells. Knock‐down/re‐expression constructs are based on shTHEMIS‐128476. Red arrowheads indicate the specific signal for endogenous THEMIS and re‐expressed THEMIS‐Strep. The higher molecular weight band observed in all lanes is a non‐specific signal.
H Relative mRNA levels of known LXRα-associated and target genes assessed with RT-PCR; n = 8/group. *P = 0.0003, #P = 0.0004, §P = 0.043, †P = 0.0009 versus Wt.
C-E. Western blot analysis for CCNA, CCNB, Cdk1 and GAPDH (loading control) protein expression in lysates from control (si-GFP) and p53-depleted (si-p53; si-p53_1) (C) MDA-MB-231 and CAL27 cell lines. Representative images are shown.
The ab initio envelopes determined by GASBOR for the (M) Kap114pyTBP complexes. Models of the (N) Kap114pyTBP complexes derived from SAXS profiles using FoXSDock and docked into the ab initio envelopes obtained from GASBOR.
D) 100 nM docetaxel treatment (24h) significantly (p = 0.0004 [***]) increases the number of pH3+ cells in the hair matrix. Unpaired t-test performed using N of 8-9 HFs from 3 patients.
a-f, Electron micrographs of MCF7.control (clone 38) (a, b) and MCF7.beclin1 (clone 17) cells (c- f) grown in nutrient-rich media (a, c) or subjected to 4 h of serum and amino-acid deprivation (b, d-f). Asterisks in e and f denote autophagic vacuoles that would be counted in the experiment shown in g. Autophagic vacuoles were defined as double-membrane vacuolar structures containing recognizable cytoplasmic contents. Scale bars, 1 µm.