EMBO/sd-character-level-ner huggingface dataset:
E. The signal intensities from pT73-Rab10 and unphosphorylated Rab10 in the input lysate co-immunoprecipitated with LRRK2 antibodies. The stoichiometry of pT73-Rab10 was calculated by dividing the pT73-Rab10 signal by total Rab10 signal (total Rab10 signal equivalent to pT73-Rab10 signal+ unphosphorylated Rab10 signal). Data are from n=3 biologically independent experiments with error bars showing ± SEM; Significance was assessed by two-tailed t-test with *** representing P<0.0005.
HMDM were stimulated directly (TNF) or primed (IL-1β, LDH) with AdV-Ab complexes as in (B). Data for each individual donor (2 total) is shown.
Figure 2. Dynamic reorganization of chromosomes during replication. (E) Log-ratio of contact maps between G2 and G1 cells (top right) and ssc1 G2 and G1 cells (bottom left). Blue to red color scales reflect the enrichment in contacts in one population with respect to the other (log2). Yellow arrowheads: inter-centromere contacts.
Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat. G. Expression of selected genes that were down-regulated in 8-month old Fmn2-/- mice was significantly increased in the dentate gyrus from mice of the Fmn2-/- Vorinostat group when compared to placebo (P < 0,05; n=4/group). Error bars indicate SEM.
A-D Wild type MEF (A), Hela (B) and PINK1 KO MEF (C) cells were treated with IU1 (48h, 100 μM) and electron microscope images were evaluated for autophagic vesicle formation. (D) bar graphs represents mean± SEM number of autophagosomes and autolysosome / cell from 3 different set of experiments; at least 40 cells were analysed from each group
The behavioural tests were recorded from wt and NPC1nmf164 mice. G. Mean ± SEM percentage of entry to the novel arm of the Y maze test (n=10 mice, 10 week-old; unpaired Student t test, **p = 0.0015). H. Mean ± SEM percentage of freezing time in the Contextual Fear Conditioning test (n=10 mice, 10 week-old; unpaired Student t test, ***p = 0.0002). I. Mean ± SEM distance covered during a 5 min period in the Open Field test (n=10 mice, 10 week-old).
qPCR analysis of Dnmt2 mRNA expression in haematopoietic tissues, normalized to GAPDH.
Model illustrating the role for Dnmt2 in the codon fidelityIn Dnmt2 wild-type cells, C38 tRNA methylation (red circle) promotes the fidelity of tRNA(Glu) and tRNA(Asp) codons, thus resulting in the translation of correctly folded proteins. In Dnmt2−/− cells, the lack of C38 tRNA methylation (gray circle) reduces the capacity of tRNAs to properly discriminate between Asp and Glu codons, leading to decreased translational fidelity, the production of unfolded proteins, and an aberrant phenotype.
(D) Colonogenic survival assay of 293A wild-type control and HMCES KO cells treated with various concentrations of hydroxyurea (HU) was shown. Seeding density with respect to control was indicated below each image. The images shown are representative of three biological repeats, each performed in duplicate.
F Single-cell transcriptomic data from aging tissues in the mouse lung from Tabula Muris Senis. Upper left panel: uniform manifold approximation and projection (UMAP) of cell identity with ATII cells represented as red dots. Upper right panel: dot plot of Ace2 expression according to age (young = 3 months; old = 30 months). Dot size represents fraction of cells expressing a given gene. Lower panel: UMAP of Ace2 expressing cells depicted as blue dots.
Mice were infected with sub-lethal dose (25 pfu) of influenza virus and assessed as follows (D) Absolute number of live CD45+ cells in whole lungs and BAL, by flow cytometry Data information: Data are representative of three independent experiments with 3-5 mice per group and represented as mean ± S.E.M Statistical significanc was determined with unpaired student's T-test
JQ1 treatment preserves photoreceptor number and function in rd10 mice. Vehicle (DMSO) and JQ1 (0.1 mM) were intravitreally injected, respectively, into one eye and the contralateral eye of rd10 mice at PN14. WT (B6) mice were injected only with vehicle. At PN18, PN21, PN24, PN27, and PN30, mice were either subjected to ERG measurements, or sacrificed for preparation of retinal sections. a Representative H&E-stained retinal paraffin sections showing a protective effect of JQ1 on ONL thickness in rd10 mice. OS/IS outer/inner segment, ONL outer nuclear layer, INL inner nuclear layer, GCL ganglion cell layer. Scale bar 50 μm. For images of PN21 and PN27, see Additional file 1: Figure S1. b Quantification for a: photoreceptor cell number per 100 μm ONL length; mean ± SEM, n = 6 mice; **P < 0.01 compared to rd10 vehicle control. c Representative ERG traces (measured at PN24, in response to 0.3, 3, or 30 cd s/m2 light intensity of flashes) showing rescue of rd10 mouse retinal function by JQ1 treatment. d Quantification of a-wave and b-wave amplitudes. ERG a-wave is the downward deflected negative response; b-wave is from the a-wave peak to positive response peak. Oscillatory potential is visible superimposed on b-wave. Data are presented as mean ± SEM, n = 10 mice, *P < 0.05, **P < 0.01 compared to rd10 vehicle control
(D) Flow cytometry analysis of CD34+CD1a- thymocytes submitted to FTOC with fetal thymic lobes deficient for Dll4 and/or Jag2 (Cre+) as indicated above the dot plots. Numbers in dot plots indicate percentage of cells for the corresponding populations. Histograms show TCRγδ expression in CD3+TCRαβ+ (blue) and CD3+TCRαβ- (red) cells.
B Control or LAPTM4B knockdown MDA‐MB‐231 cells were transfected with His‐tagged ubiquitin, starved, and stimulated with 100 ng/ml EGF for 30 min. Total ubiquitinated proteins were purified from whole‐cell lysates by Ni‐NTA agarose and analyzed by Western blot.
RNA pulldown assays interrogating putative GUARDIN-associated proteins identified in (A) from whole-cell lysates of A549 and HAFF cells. BRCA1, BARD1 served as positive controls and β-actin served as negative controls.
Both maps show well-resolved protein features including water molecules (left, right). Side-chain features of Y70, I121, R46 and F35 residues at Ca2+/acidic pH. Snapshot of RNA map features with Mg2+ ions in water conditions.
(F) Accumulation of H3cs.1, a specific N-terminal cleavage product of H3, in OIS cells. See Materials and methods for details of time course. Western blotting was performed using the same cellular lysates as in Fig. S4 B, and the same lamin A/C panel is shown in both figures.
D, Cytoplasmic and nuclear proteins from vector or INSL5overexpressing cells were separated and subjected to immunoblot as indicated. The nuclear marker Lamin B1 and the cytoplasmic marker GAPDH were used to demonstrate the purity of fractions.
B. Representative traces for C-F, showing evoked AMPAR- and NMDAR-mediated EPSCs (collected at −60 mV and +40 mV, respectively) in paired uninfected (black traces) and EGFP-GSK3α-expressing neurons (green traces) in C57 wt or tauKO slices.
F- Box plot showing Pol II pausing duration in RPB1-52R and RPB1-25R cells for genes encoding major isoforms with constitutive first exon longer than 100 bp. p value<2.2e-16 (Mann-Whitney U test) Box limits are the first and third quartiles, the band inside the box is the median. The ends of the whiskers extend the box by 1.5 times the interquartile range. Two independent biological replicates were analyzed.
(f,g) Top: IBs for NBR1, p62 and actin in control and NBR1 knockdown (NBR1 KD #161) SY5Y cells (f), and in control and p62/NBR1 double knockdown (Double KD #A or #B) SY5Y cells (g). Bottom: autophagic clearance of GFP-ANK1-p38 Agm in the same cells. For all densitometric analyses, values are mean+s.e. (n=3). *Significant versus serum+ condition. See also Supplementary Fig. S8-S11.
E. Aliquots of the supernatants were treated with or without Endo-H and electrophoresed under reducing conditions. The blot was decorated with anti-µ antibodies. N563-glycans acquire Endo-H resistance in µsL566A and µsC575A, but remain largely sensitive in wild type µs.
G Expression of lineage markers after embryoid body (EB) formation and spontaneous differentiation in nRH13 cells. *P<0.05, ***P<0.001 (t-test). Data presented as mean ± SD (n=3).
(e) Analysis of IRGM (green) and COX IV (red) intensity as a function of distance along the line shown in the inset. Image in inset corresponds to panels J-L in d. Uncropped images of blots are shown in Supplementary Information, Fig. S8.
Calu6 (mesenchymal) and H1975 (epithelial) NSCLC cell lines after treatment with fibronectin for 24 hours. Cells were then harvested, and lysates were immunoblotted for the indicated proteins.
(D) The data modalities that supported the rCCS status of ESR1 and the proportion of cell lines having that evidence in the ER+ cell lines (n=20).
DNA methylation levels of the HES5 promoter region of SH97Q cells treated with DHT and RG108.
(a) The gross anatomical views of representative 4% paraformaldehyde-fixed livers and quantification of liver index. (Data are shown as mean±s.e.m., P values are indicated on the figures, unpaired Student's t-test, n=3 mice each group). Scale bar, 1 cm.
WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) showing (U) total APP (top blot), CTFs (2nd blot) and phospho-tyrosine (3rd blot) relative to actin (N = 9).
iPSC-derived HE, EHT and HSC-like cells were sorted, cultured for 1 day and analyzed by scRNAseq. (b) Heatmap showing expression levels of endothelial and hematopoietic genes in HE, EHT and HSC-like populations.
(A) Western blots of oskar mRNP components (Staufen, Bruno and Y14) and motor associated proteins (Khc, BicD, Dic) co-immunoprecipitated with EmGFP-Tm1-I from ovarian lysates. Protein marker bands and their molecular weight in kDa are indicated.
(i) The bar graph shows the genes most strongly correlated with SSTR2 belonging to the GO category "transcription regulators". The dotted line marks a correlation coefficient of zero.
I Representative images of human NTM granuloma from lymphnodes, immunohistochemistry for p53 (brown), nitrotyrosine (red) and hematoxylin counterstaining.
(E) Polarized Calu-3 were inoculated with 0.5 TCID/mL of a SARS-CoV-2 isolate (hCoV-19/Italy) either directly or in presence of antibodies against ACE2 or upon pre-treatment with LMWH enoxaparin (250 IU/mL) for 30 min at 37°C. Virus was detected by lysing after 48 hours through quantitative real-time PCR of viral RNA (E) and virus production was determined by detection of viral RNA in supernatant using quantitative real-time PCR (F). Data information: Data show the mean values and error bars are the SEM. Statistical analysis was performed using (E, F) ordinary one-way ANOVA with Tukey's multiple-comparison test. *P≤0.05, **P≤0.01, ***P≤0.001, ****P≤0.0001 (n=3 donors measured in monoplo). TEER: Transepithelial electrical resistance.
(G-H) Immunofluorescent staining of γ-H2AX, 53BP1 and Cleaved Caspase-3 in the intestinal epithelium of KLF4 loxp/loxp mice with injection of AAV7-mCherry or AAV7-Cre-mCherry followed by treatment of γ-irradiation. Tissues were collected from sham mice and mice at different time after exposure to γ-irradiation and then staining with indicated antibodies. (G) Quantification of γ-H2AX, 53BP1 and active Caspase-3 -positive cells based on the Immunofluorescent staining results presented in H. Data are mean ± SEM; n=4 per group; p = 0.0023 (r-H2AX), p = 7.9x10-4 (53BP1) p = 5.5x10-3 (Active Caspase-3). one-way ANOVA was used for the statistical analysis. Scale bars, 60 μm.
(F) Heat map showing MS analysis of AhR pulldown protein from MC38 cells treated with MBELNs in combination with proteasome inhibitor, MG132. Data are represented from three technical replicates.
C BGL3 promotes BARD1-HP1γ (up panel) and BARD1-RAD51 (middle panel) interactions in vitro. GST-HP1γ, GST-RAD51, and FLAG-BARD1 were overexpressed and purified from cells as indicated in Methods. FLAG-BARD1 was divided into two equal parts, one part was used for BARD1-HP1γ interaction analysis (up panel), and another part was used for BARD1-RAD51 interaction analysis (middle panel). BARD1-HP1γ (up panel) and BARD1-RAD51 (middle panel) interactions with or without BGL3 were respectively detected by GST pull-down assays, here GST was used as a pull-down control.
HEK293T cells transfected with GST-tagged empty vector, NEMO-WT, or NEMO-K326R, with or without Strep-tagged MARCH2 were infected with VSV-GFP. , fluorescence absorbance (E)
Quantification of autophagosome-free lysosomes in (E). Experiments were performed three times, and one representative experiment is presented here.
Gene ontology analysis (top 5 categories) of mis-regulated proteins. The top 5 categories are presented.
(c) Total locomotor activity was assessed as the average number of beam crossings per 30-min bin per fly. Htt93Qex1-expressing flies (n = 29) have reduced locomotor activity compared to controls (***P 0.001; n = 30 (WT (w118)); n = 32 (mGpx1)), which is restored by mGpx1 (**P 0.01; n = 32). Comparisons were performed by Kruskal-Wallis one-way ANOVA.
(E-F) Still images from Movie EV4 of facial lymphatic development in a lyve1b:EGFP kdrl:nlsmCherry compound transgenic from 48-62 hpf showing that after the CCV-derived FLS fuses to the PHS-L, these take over as the leading tip cells (orange asterisks), with one PHS-L migrating anteriorly to fuse with PHS-LPA (yellow asterisk), and others migrating ventrally to fuse with the VA-L (purple asterisk) After the PHS-derived portion (orange outline) of the FLS (green outline) fuses to the VA-L (purple outline), migration of the entire facial lymphatic pauses to allow for lymphangioblast proliferation (dark blue and red parent cells, light blue and pink daughter cells) before resuming migration anteriorly along the ventral base of the eye
E. Calculated percentage of vesicles positive with tubular structures (n>30 vesicles analyzed from cells from n=3 biologically independent experiments) are shown. Each dot represents one vesicle, with significance assessed by Mann-Whitney test. ** represents P<0.01. Error bars represent ± SEM.
293T cells treated with DMSO (B) or H2O2 (200 µM, 2 h) (D), were harvested for mitochondrial isolation. Purified mitochondria were treated with the indicated gradient concentration of proteinase K for 20 min on ice, and then were analyzed by Western blotting with anti-ATAD3, anti-Tom20 (OMM), anti-Tim23 (IMS), and anti-HSP60 (matrix). Relative protein levels of proteins in (B) or (D) were further evaluated by densitometry analysis using ImageJ software. Relative trends of proteolysis of indicated mitochondrial proteins from DMSO- or H2O2-treated cells were shown (C and E). Data are presented as mean ± SD (n = 3 independent experiments).
12-week-old male WT ( Prom1+/+) and KO (Prom1-/-) mice were fasted for 4 hours and intraperitoneally injected with glucagon. (D) The cAMP concentration in the liver after a 5 minutes glucagon treatment was determined using the cAMP assay kit (2 mg/kg body weight, n = 3/group).
D) Hits mapped onto the 187 human genes used as the basis for screening in D. melanogaster. Protein-protein interactions were identified from the set of 409 proteins identified in mammalian cells[16]. For gene knockdowns that inhibited autophagy, dark red indicates that two amplicons had a score < -0.5, while light red indicates that only one amplicon had a significant SSMD score, but that it was < -1. For gene knockdowns that increased autophagy, dark blue indicates that two amplicons had an SSMD score > 0.5, while light blue indicates that only one amplicon had a significant SSMD score, but that it was > 1.
(A) Representative cross-sections of draining LNs (dLNs) from mice 7d post immunization with HEL-OVA/CFA following adoptive transfer of BHEL and transduced CD4OT-II cells. dLN were cryosectioned and stained with fluorophore-conjugated antibodies against GL-7 to reveal GCs (green), CD21/35 to stain for follicular dendritic cells (FDC, red) and Hoechst to stain for cell nuclei (blue). Scale bar, 250µm. (B, C) Quantification of the number of GCs relative to B cell follicles (B) and size of GC (C) on confocal micrographs as shown in A. Shown are mean values with SD from dLNs from three mice in two independent experiment. Each dot represents one LN (3 LNs/mouse) in B and one GC in C.
F Schematic overview of synchronization experiment. Cells were arrested at the onset of S phase with 2 mM hydroxyurea (HU), and induction of E2F8WT or E2F8K/Kmut was started 12 hours prior to release from HU.
(A) WB analysis of LC3 and p62 (an autophagy substrate) was performed on WT and MPS-IIIA brain samples at indicated ages. WB quantitation was shown.
E WT, ADAP−/−, or SKAP55−/− OT-I CTLs were pretreated with the DMSO control, 10 μM PP2 or 75 μM 2APB, then stimulated with OVA257-264-pulsed EL-4 cells for 4 h to examine surface PD-1 expression (mean of triplicates ± SD).
B. Immunoblot analysis (IB) of GST-pulldown samples with deletion mutants of FUS‑NTD‑GST as baits with/without cell extract (C.E). ARID1A and BRG1 were used as tracers of SWI/SNF binding. Coomassie staining of recombinant proteins are shown in the lower panel. Amino acid numbers are indicated
B ddPCR detection of ACE2 mRNA expression levels in early passages (PD 22.37) and late passages (PD 140) human bronchial epithelial cells (HBEC) (n = 6 replicates per group).
(i) Calpain resistant Atg5Δ191-196 was unable to sensitize HeLa cells lacking endogeneous Atg5 (due to gene silencing, see Fig. 1c) to staurosporine-induced cell death. Values are means ± s.e.m. of three independent experiments (18 h cultures).
(C) Thiosulfate levels in urine and (D) plasma normalized to protein amount. Error bars represent SDs of 9 animals per group (urine) and 6 animals per group (plasma).
ApoEVs isolated after IgG1 and tigatuzumab treatment (MDA-MB-436) were run on western and blotted against CD63 and PD-L1.
Figure 5: Memory decline in 8-month old Fmn2 -/- mice correlates with deregulated transcriptome plasticity F. Cytoscape-generated network of genes deregulated in 8-month old Fmn2-/- mice.
(D- E) 3D view of the CTLD4 domain of MRC-1 showing the surface location of the peptides P2 and P3 (in pink). Acidic and basic amino acid residues are shown in red and blue respectively. Indicated in green is the calcium binding site.
Quantifications of nuclear/cytoplasmic Ebd1 (F) In (F), n=1044, 14 BL at 0h ALH; n=712, 10 BL at 24h ALH and n=1122, 11 BL. Data information: Data are presented in F, as mean ± SD. n numbers in F, were total NSCs counted with total brain lobes measured, while each brain lobe was considered as one biological replicate. Statistical analyses were done comparing two different genotypes using Mann-Whitney test F). statistical analyses were done comparing the percentage at later time points with the ones at 0h ALH. ns: non-significant; *P < 0.05; ***P < 0.001.
Control or ATAD3B KO HeLa cells stably expressing mito-Keima were treated with 4 mM 3-NPA for 2 h and imaged with 458 nm (measuring mitochondria with a neutral pH) and 561 nm (measuring mitochondria with an acidic pH) laser excitation for mito-Keima by confocal microscopy. Scale bar, 10 µm. Quantification of the relative ratio of red to green fluorescence intensity (561 nm/458 nm) of the cells described in (B). Data are presented as mean ± SD (n = 3 independent experiments, 20 cells per experiment), statistical significance was assessed by two-tailed student's t-test, N.S., not significant, **p < 0.01.
D BAK-6H oligomerisation on liposomes involves its BH3 domain. Liposomes were incubated with BAK-6H (150 nM) together with cBID (90 nM). Antibody recognising the BAK BH3 domain (4B5) or α1-α2 loop (7D10), as shown on the structure of BAK (PDB:2IMS), were added (2.4 μg/μl) either prior to (pre) or after (post) incubation with cBID for 60 mins. BAK:Ab complex is indicated (arrowhead). 7D10 which recognises the activated form of mBAK (Iyer et al., 2016), bound to and gel-shifted BAK when added either before or after activation with cBID. In contrast, 4B5 failed to appreciably gel-shift inactive BAK (lanes 3 and 5) or BAK that was already activated (lane 6), but gel-shifted BAK when present during cBID activation (lane 4). Liposome permeabilisation was assessed after 20 min incubation with cBID (90 nM), BAK-6H (150 nM) and antibodies 4B5 (2.5 μg) or 7D10 (2.5 μg). Data is presented as mean of 2 independent experiments with percentage release relative to detergent-lysed liposomes at a timepoint when permeabilisation with BAK and cBid was approximately 50% of detergent-lysis maximum.
HSF1 expression was diminished in MCF10A cells for 48 hours using siRNA prior to treatment with either DMSO or RSL3 at the range of concentrations shown. Cells were assessed for viability after 24 hours. Absorbance was normalized to DMSO control. Shown are three independent replicates with standard deviation (n=3 experiments per group). P‑values were obtained by unpaired Student's t‑test with *P<0.05, **p<0.01, ***p<0.005. Exact p‑values are reported in the Appendix Table S1.
(B-C) Summary of GALC activity in spinal cord (C; n=3 blocks/animal) samples from JT02 and JV02, as well as from WT and Krabbe UT controls. Data in A-C are represented as floating bars (min to max, line at mean; n=2-6 blocks/slice). Number of blocks analysed/animal: 16 (WT UT), 24 (JT02), 22 (JV02). GALC activity in Krabbe UT samples is < 0.001 nmol/h*mg; n=3 blocks. Kruskal-Wallis test and Dunn's multiple comparison test; *p<0.05, ***p<0.001 vs WT UT.
D Upper panel: in vivo growth of tumors derived from intradermal injection of shTINCR-2 or shSCR WM902B cells in NSG mice. 600,000 WM902B cells per mouse were inoculated. Tumor volumes (mean±sd) were measured 8 weeks after transplantation. Results from two independent experiments (four animals per group) are shown. Statistical analysis between control and TINCR-silenced groups was performed using the Student t -test (**=p<0.01). Lower panel: qRT-PCR analysis of TINCR RNA expression in tumors derived from in vivo transplant of shSCR and shTINCR WM902B cells (8 weeks after injection). TINCR RNA levels relative to L32P housekeeping gene and control (mean±sd) from four biological replicates (animals) from both experiments are shown.
D Representative RNAscope image of sections from patient ILCs (n=5) stained with anti-LOXL1 probes (red) and counterstained with DAPI (blue). Scale bars; 50 μm.
(L-O) Grh1 and Gvp36 involvement in AmphoB-induced autophagy-like proteolysis. (L, M) Representative electron microscopy images of grh1Δatg5Δpep4Δ (L) and gvp36Δatg5Δpep4Δ cells (M) treated with AmphoB (2.5 µg/ml, 24 hr). AP-like and AB-like structures were absent. (L) A unilamellar Golgi cisterna was observed in the cytoplasm (dotted square). Scale bar = 1 µm. (M) Formation of a Golgi stack, but not Golgi curvature, was observed (dotted square). Bar = 0.5 µm.
D-E. Unlike deletion of Atg11, deletion of other known selective Atgs required for the CVT pathway (Atg19), mitophagy (Atg32) and pexophagy (Atg36), does not result in increase of GFP-Snc1-PEM protein level (D), intra-cellular accumulation of GFP-Snc1-PEM, (E), and induction of the UPR response (F). Wild type (WT), atg19Δ, atg11Δ, atg32Δ, and atg36Δ mutant cells overexpressing GFP-Snc1-PEM were analyzed as described for panels A-C, respectively. E. Shown from left to right: DIC, GFP, and % cells with intracellular Snc1-PEM structures. +/- and error bars represent STDEV. Results in this figure represent at least two independent experiments.
F. UPR is induced in atg11∆, but not in atg9∆ single- and atg9∆ atg11∆ double-mutant cells overexpressing GFP-Snc1-PEM.
D Schematic of all identified proteins (blue circle) and cell surface proteins (pink circle). Cell surface/plasma membrane proteins were identified based their GO annotations; their distribution is shown in a pie chart (top).
B. The AUC of the ROC curves in A are shown as large dots, compared to random permutations (which preserve the counts of each cause and effect but randomize their pairings) of the edge list which are shown as small dots and a boxplot of these null AUCs. Permutations with values systematically in excess of a value of 0.5, as seen when predicting genetic interactions with rise time, are likely due to hub effects where genes that tend to be predicted regulators of many targets also tend to have interactions.