EMBO/sd-character-level-ner huggingface dataset:
Dimethyl-labeling analysis of 8-day-old mouse bone marrow tissue. Proteins that were down-regulated (< twofold change) in Dnmt2-deficient cells are indicated in red, and up-regulated proteins (> twofold change) are shown in green. Nestin and periostin are marked with arrows.
(E) P-Taf12 was followed in WT, igoS64A, pab1Η, and pab1Η igoS64A strains, grown in rich conditions (R) or starved for 45 minutes (S). An anti-Rpb1 IB is shown as a control for loading. (D,E) The signal intensities of P-Taf12 and total Taf12 were quantified in each strain and condition. Shown below each blot are average measurements of 3 independent experiments (n = 3). A short and a long exposure of the FLAG IB are shown to detect total Taf12 and P-Taf12, respectively, within the linear range of the chemi-luminescence signal. The star (*) symbol labels an unspecific band detected by the S. pombe antibody in S. pombe.
Quantitative RT-PCR measurement of Fgf21 and GDF15 expression in GC muscle of 6-month-old control, HSA-Cre untreated and HSA-Cre TUDCA-treated mice.
RNA sequencing (RNA-seq) of week 15 COs and transcriptome analysis (WT: n=2, KO: n=4). Gene-set enrichment analysis (GSEA) revealed enrichment of genes related to regionalization of the organoids, and decreased expression of genes related to negative regulation of the cell cycle.
(H) Predominant cytoplasmic localization of H3cs.1 in senescent cells. α-Tubulin and lamin A/C were used as fractionation controls for cytoplasmic and nuclear fractions, respectively.
(i) Plasma levels of triglycerol (TG) in WT and Atg5 Tg mice. The mice were fasted for 3 h before measurement. Young mice (4-week old, n=8); old mice (18-month old, n=8). ***P0.0001 versus control; Student's t-test
(B) WDR63 mRNA and protein levels in A549, H292, and HCT116 cells transduced with control (shctrl) or p53 (shp53) shRNA. Data shown are mean ± SD; n = 3 independent experiments. ***, P ˂ 0.001; two-tailed Student's t-test.
(C) RT-qPCR quantification of relative pri-miR-21 and miR-21-3p levels in the epidermis (left and middle), and of relative miR-21-3p in the dermis (right) of acutely irradiated (Ac-UV; +) and non-irradiated (-) Ppard +/+ and -/- mice. Pri-miR-21: Ppard +/+ Ac-UV vs Ppard -/- Ac-UV P = 0.022; miR-21-3p: Ppard +/+ no UV vs Ppard +/+ Ac-UV P = 0.017, Ppard +/+ Ac-UV vs Ppard -/- Ac-UV P = 0.008. N=3-4 animals per group, one representative experiment is shown out of three independent replicates.
(B) cGTPase rearrangements in MgGDP binding. Displayed is the MiroS‐MgGDP structure, with select residues from the aligned apo‐MiroS structure shown in orange. GDP is shown as sticks (2Fo‐Fc map, 1.2σ), and Mg2+ as a purple sphere. In the apo state, D505 in the Switch II 503DIDV506 motif is far from the nucleotide‐binding pocket and is hydrogen bonded to R507, which is also stabilized by interactions with P512. In the MgGDP‐bound state, the D505 side‐chain rotates ∼7 Å to interact with the β‐phosphate (arrow), locking the Switch II loop in a β‐strand conformation and extending Gβ3. V506 rotates away from the nucleotide‐binding pocket, and both R507 and Y537 become solvent exposed. cGTPase, C‐terminal GTPase; Sw I/II, Switch I/II; P loop, phosphate‐binding loop.
H, I. Representative energy-dispersive X-ray spectra of (H) cytosol and (I) condensate. Black arrowheads indicate Fe (Kα) peaks.
(C) LncRNA CRNDE expression in SGC7901 cells incubated with monocytes-exo or M2-exo was measured by qRT-PCR. **P<0.01 vs. monocytes-exo. Data information: The results shown are from three biological replicates. Data are expressed as mean ± SD. Student's t-test.
(C) Protease protection assay of ykt6-11 and dsl3 mutants. Lysates of atg1∆, ypt7∆, ykt6ts and dsl3ts cells carrying a CEN plasmid expressing GFP-Atg8 were grown at 37°C and subjected to the protease (PK)-protection
(A) Ovaries of adult female flies (w1118, alix1 and alix-l/CyO; alix1) were stained with rhodamine-phalloidin (red), anti-α-tubulin (green), anti-Cnn (white) and Hoechst (blue). Typical confocal micrographs of metaphase FECs are presented and the apical membrane facing the egg chamber lumen is indicated with *. Scale bar, 5 μm. The MS orientation was measured and the graph shows the average percentage of FECs (w1118, n=45, alix1, n=45, alix-l/CyO; alix1, n=39, from three independent experiments) with the indicated relative spindle angle (±S.E). Statistically significant difference is indicated as ***p<0.001 (ANOVA)
F Electron micrograph of a section through the larval epidermis to show the highly folded lateral junction between two epidermal cells (magenta and cyan). Left, cartoon; middle, false colouring; right, original image. C: cuticle; M: mitochondrion; BL: basal lamina; AJ: adherens junction; SJ: septate junction; GJ: gap junction, N: nucleus, Mv: apical microvilli connecting the cuticle to the cell.
YAP driven aberrant sphere formation of MCF10A cell lines is ablated by AIB1 knockdown, but further enhanced by ANCO1 knockdown. Indicated cell lines were plated on Matrigel and allowed to form mammospheres for 7 days. 10x and 40x magnifications shown, Scale bar = 200μm.
(E) Bar graph quantifies percentages of mitotic cells exhibiting multipolar spindles upon CPAP-WT or CPAPΔT expression. (N)=3. Error bars, mean ± SEM. Unpaired t-test **P < 0.001
(F Western blot analysis for protein levels in P493-6 cells that overexpressed empty vector (EV), ALKBH5, or FTO and were then treated with Tet or not (F) HPRT1 and β-actin served as negative and loading controls, respectively. Data are representative of at least three independent experiments.
Sample recordings from 7-week-old hESC-derived Cerebral Organoids (COs). Mean spectral power of week 7 WT and KO COs in baseline conditions. The line marks 0.25-1 Hz frequency range. Statistical significance was determined using two-tailed unpaired Welch's t-test (WT: n=14 slices, 5 organoids, 3 batches. KO: n=14 slices, 8 organoids, 3 batches).   Normalized area under the curve of the mean spectral power in (B) for the 0.25-1 Hz frequency range. Data represented by mean ± SEM. Statistical significance was determined using two-tailed unpaired Welch's t-test. The numerals in all bars indicate the number of analyzed slices and organoids (i.e. slices (organoids)).
(B) RT-qPCR analysis of MERVL, MSR and L1MdA in Foxd3 cKO cells, Foxd3 cKO cells over expressing full length FOXD3 or FOXD3 M1 without and with 4-OHT. Data is represented as fold change relative to respective untreated cells after normalizing to Gapdh. The average data for 3 biological replicates is plotted, error bars represent standard error mean (SEM). Asterisks indicate statistically significant differences. (**: p< 0.005, *: p<0.05 paired t-test).
(A−I) Induction of GOMED in Atg5 KO MEFs by CBM treatment. (A, B) EM analysis revealed the formation of AP-like and AL-like structures. Atg5 KO MEFs were treated with CBM (2 mM) for 3 hr. A representative low-magnification image (A) and high-magnification images (B) are shown. Scale bar = 1 µm (A) and 0.2 µm (B). The arrowheads and arrows indicate AL-like and AP-like structures, respectively.
(C) DHE transfer between liposomes by purified GRAMD1b proteins. Left: Representative time course of DHE transfer from LPM to LER mediated by either wild-type GRAMD1b proteins (WT), mutant GRAMD1b R189W proteins (R189W), mutant GRAMD1b R189W/R191A proteins (RW/RA), or buffer alone as indicated. Methyl-β-cyclodextrin (MCD) at 1 mM was used to determine DHE equilibration. Transfer of DHE from LPM to LER resulted in a decrease in fluorescence resonance energy transfer (FRET) between DHE and DNS-PE in LPM. A series of liposomes with different DHE mol% were prepared to plot a calibration curve to convert FRET signals to DHE molecules transferred (see Appendix Fig S2D and Materials and Methods). Right: Values of DHE transfer rate of GRAMD1b (WT), GRAMD1b (R189W), and GRAMD1b (RW/RA), as estimated by the FRET-based lipid transfer assay [mean ± SEM, n = 6 independent experiments for WT, n = 3 independent experiments for R189W and RW/RA
(h) FACS-sorted HE cells were subcultured with or without DCA (3 mM) for 2 days on coverslips. Staining intensities of H3K9 acetylation and H4K5, 8, 12, 16 acetylation were assessed by confocal microscopy imaging and fold change ± SEM compared to the control is shown (n=3 biological replicates). Data information: ns, not significant, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001
(A) Western blot of Beclin‐1 and FACS profiles following siRNA treatment in HeLa cells and cells stably expressing a HA‐Beclin‐1 construct resistant to the siRNA targeting endogenous Beclin‐1.
Quantitative RT-PCR expression analysis of miR-17 in human CB CD34+Lin- after 5 days, respectively, of coculture on OP9 stromal cells expressing different Notch ligands Graphs show mean expression, relative to the geometric mean of SNORD61, SNORD95 and RNU6-2 and relative to the OP9-DLL1 cultured cells (n=2 independent experiments with different donors; error bars indicate SEM - the two data points are shown).
Two gRNAs flanking the Dl Exon 2 were used to replace the exon with a modified version where 5 amino-acids in the β1-2 loop were removed. Red lettering highlights the genomic sequence of the β1-2 loop.
Hepatic CREBH mRNA (B) levels in the WT and L-HRD1 KO mice. (n=6 for each group). Data information: The data are representative of three independent experiments (mean ± s.d.).
ChIP-qPCR analysis of Rpc37 around SPCTRNAARG.10 gene in the strong terminator mutant (mean ± standard deviation from 4 biological replicates).
I, mHEVc were treated with or without Akt inhibitor IV and infected with T. gondii. 1 h post infection cells were treated with or without leupeptin plus pepstatin (Lys inhibitors). Monolayers were examined microscopically 24 h post-challenge.
(A) Wild type primary hepatocytes were infected with an adenovirus harboring sh-control (sh-Con), sh-radixin (sh-Rdx), GFP (Ad-GFP), and/or sh-resistant wildtype radixin (Ad-RdxR) or AKAP-dead LPTD mutant of radixin (Ad-LPTDR) for 24 hours.
Testing the SARA-CoV-2-RBD specific human monoclonal antibodies (D) using the purified SARS-CoV-2 particles. The control plasmas 1 and 2 were obtained from a patient recovered from influenza A virus infection and a healthy volunteer, respectively. The control monoclonal antibody is a human monoclonal antibody specific to influenza A virus generated by our laboratory. The PBS control was serum-free.
(h) The NRBF2 KO MEFs were transfected with CFP, NRBF2-CFP, dMIT-CFP or dCCD-CFP for 24 h and then followed by co-immunostaining with GFP and WIPI2 antibodies. (i) The WIPI2 puncta number per cell in GFP-positive cells were counted and quantified. (Data are shown as mean±s.e.m., P values are indicated on the figures, independent samples Kruskal-Wallis test followed by pairwise comparisons, n=30 randomly selected cells, a representative result from two independent repeats). Scale bars, 20 μm, or length indicated on the figure. CM, culture medium.
B) KLN murine lung sections were stained with H&E or with Periodic Acid Schiff (PAS) and Alcian blue (AB). Scale bar, 50 μm.
Representative Western blots illustrating the expression of SMC6 and of monoubiquitylated FANCD2 in protein extracts from HeLa cells transfected with the indicated siRNAs and treated 48 hours after transfection with HU (5mM, 18 hours) or Mitomycin C (200 ng/ml, 18 hours). Vinculin is used as loading control.
C GOT2 deacetylation is dependent on SIRT3 catalytic activity. Flag‐tagged GOT2 was ectopically expressed in HEK293T cells together with HA‐tagged wild‐type SIRT3 and a catalytically inactive mutant, SIRT3 H248Y. GOT2 proteins were purified by Flag beads, following Western blot to detect GOT2 K159 acetylation.
(D) Transcriptional (RNA-seq) vs. translational (Ribo-seq) control of mTOR-regulated mRNAs.
(a) Stacked bar plots of all 11 and 12-member (full) multi-species communities. The text above each subplot denotes the absent organism in the community. Time and relative abundance are represented on the x and y-axis of each subplot, respectively. Colors represent different organisms in the community. (b) Difference in community assembly for single-species dropout communities. Difference in community assembly was computed as $\sum_{i = 1,\ }^{11}{\frac{1}{7}\sum_{j = 1}^{7}{({\widehat{v}}_{ji,FULL} - v_{ji,X})}}^{2}$ where i and j represent species and time points, respectively. X represents a single-species dropout community lacking the organism X. v̂ denotes the renormalized relative abundance of the shared set of species in the full (12-member) and single-species dropout community. Here ${\widehat{v}}_{i} = \ \frac{v_{i}}{\sum_{i\ \in C}^{}v_{i}}$ where C denotes the set of 11 shared organisms in the full and single-species dropout community. Data points represent biological replicates (n = 6, circles) and the mean of biological replicates (blue squares), respectively. (c) Box plot of the Pearson correlation coefficient for three model training sets (left) including T1: monospecies (M); T2: M and pairwise 1 (PW1); and T3: M, PW1 and pairwise 2 (PW2). On each box, the red line represents the median, the edges of the box are the 25th and 75th percentiles, the whiskers extend to the most extreme data points and the outliers are plotted as red crosses. (d) Box plot of the sum of mean squared errors for the model predictions of the time-resolved measurements of multi-species communities trained on T1, T2 or T3 training sets. On each box, the red line represents the median, the edges of the box are the 25th and 75th percentiles, the whiskers extend to the most extreme data points and the outliers are plotted as red crosses. (e) Comparison between model prediction based on T1-T4 and experimental data for each organism in the full community as a function of time. On each subplot, the x and y-axis represent time and relative abundance of each species, respectively. Data points (red) and lines denote experimental data and model predictions based on T1-T4. Species names are displayed in the upper left corner of each subplot. Error bars represent 1 s.d. from the mean of six biological replicates.
(B) Dot plots quantifying total photon flux during in vivo whole body as well as ex vivo lung and lymph node bioluminescence imaging (mean ± SD, nIgG = 8, nAB-Tie1-39 = 9 mice). *, P<0.05; **, P<0.01 (two-tailed Mann-Whitney U test).
Figure 2: FMN2 is highly expressed in mossy fibers and is required for synaptic depotentiation.E. Left panel: Representative images showing the co-localization of FMN2 (green) and Synaptoporin in the mossy fiber pathway in low and high magnification. Right panel: Immunoblot analysis of hippocampal synaptosomes (Syn) compared to cell homogenate (H) showing that FMN2 is present in the pre-synaptic compartment. Synaptophysin was used to confirm enrichment of synaptosomes. For all experiments parasagittal brain slices from 14-21 day old mice were used. Cere, cerebellum; Hip, hippocampus, mf; mossy fiber, str. Luc.; stratum lucidum, cc, corpus callosum.
ISG qPCR from PMA-treated THP-1 shSAMHD1 cells transduced for 24 h with LPV-treated HIV-1 GFP viruses (0.1 U RT/ml red line, 0.5 U RT/ml blue line).
Indicated tumors were harvested, fixed, and stained for the proliferative marker mKi67. Three random fields from each tumor were counted for mKi67 positivity, and are plotted as a % of total cell number, n = 5 (right: representative images). Images were taken at 400× magnification.
(B) Heatmap with hierarchical clustering of RNA-seq data from biological replicates of FusΔNLS/ΔNLS (N=5) and control littermates (N=4), showing genes differentially regulated between both genotypes among which 237 are upregulated and 549 are downregulated in FusΔNLS/ΔNLS animals
(C) HeLa cells were transfected with control, ALIX, MAP1S or ALIX+MAP1S siRNA and the expression of ALIX, MAP1S and GAPDH (loading control) was determined by Western blotting analysis. Representative results are presented
D Mutation of BH4 promotes BAK activating conformation change. Cells were treated with doxycycline (3 h) to induce BAK expression followed by incubation with BH3-mimetics where indicated (for 2 h) and conformation change of BAK was assessed by intracellular flow cytometry with an antibody that recognises activated BAK (G3172).
(H) The FOXO3a-mediated transcriptional activity was measured with a luciferase reporter under the control of a FOXO-response element promoter. HEK293T cells were transfected with shRNAs for control, LSD1, UBE4B, or both LSD1 and UBE4B, followed by transfection of the luciferase reporter together with a constitutively active form of FOXO3a (TM) 72-96 h later (n = 6). Data represent means ± SEM. The numerical data used to make this figure can be found in S1 Data.
(E, F) The ab initio shape envelopes of the individual xrRNA1s (E) and xrRNA2s (F) of DENV2 (cyan), ZIKV (red), WNV (blue) and MVEV (green) are fitted with the homologous atomic models built by ModeRNA.
Dose-response curves of IL-12 secretion in BMDCs pulsed for 60 min with the indicated lipids, followed by stimulation with R837 (5 μg/ml) for 18 h. Toxic concentrations of lipids were excluded from analysis. Mean ± SEM of triplicate determinations are shown.
Hepatic growth hormone signaling target genes mRNA levels in the WT and L-HRD1 KO mice. (n=5 for each group). Data information: The data are representative of three independent experiments (mean ± s.d.). *: P<0.05. **: P<0.01 by unpaired student's t test.
Schematic representation of the experimental workflow. Patient-derived HCC cells or Huh7-Luc cell lines were orthotopically transplanted into livers of B-NSG mice. Then mice were treated with scramble RNAs, ASOs for HAND2-AS1 and/or combined with siRNAs for BMPR1A.
A. Hcp release assay. HA-tagged Hcp (HcpHA) release was assessed by separating cells (C) and cell-free culture supernatant (S) fractions from 109 wild-type (WT), ΔtssM cells or ΔtssM cells carrying the AHT-inducible FLAG-tagged tssM-borne plasmid (tssM+) treated (bulgecin) or not (NT) with bulgecin A prior to tssM gene induction. Proteins were separated by 12.5%-acrylamide SDS-PAGE and the periplasmic TolB protein (control for cell lysis), HcpHA and FLTssM were immunodetected using anti-TolB (middle panel), anti-HA (lower panel) and anti-FLAG (upper panel) antibodies. Molecular weight markers (in kDa) are indicated on the left. The experiment was performed in duplicate and a representative result is shown.
(C) Pacs1+/+ and Pacs1−/− FOB cells were labeled with Indo-1 and stimulated in Ca2+ free buffer with 5 mcg/ml anti-IgM (black arrowhead) to assess ER Ca2+ efflux. Then, 2 mM Ca2+ was added back to assess SOCE. Kinetic traces normalized to baseline from three independent Pacs1+/+ and Pacs1−/− pairs are shown with the mean Ca2+ flux overlaid in bold.
Human DCs were incubated with a non-cytolytic dose (0.2 μg/ml) of purified SLO for 45 min. Immunofluorescence staining shows that SLO (green) co-localize with MRC-1 (red) in DCs and EEA-1 (purple, early endosomes). All scale bars, 5 μm. Images are representative of three independent experiments.
B Sample processing. Samples were lysed with mild detergent (0.8% NP-40), soluble proteins were extracted and digested to tryptic peptides. Peptides were labelled with TMT labels and pooled. After offline reversed phase fractionation, samples were analyzed with mass spectrometer.
D, Analysis of glycolytic gene expression by immunoblot in INSL5 overexpressed or knock-down cell lines.
(E) Viruses were detected by IFA using the patient's plasma, and plasma from a healthy control was used as negative control. Scale bar, 100 μm.
(G) Z-disc intervals (sarcomere length) of slow skeletal muscle at 1 dpf in smyhc1+/+ (n = 380), smyhc1R673H/+ (n = 293), and smyhc1R673H/R673H (n = 268). Distance between z-discs was measured in anti-α-actinin stained slow skeletal muscle fluorescence images. The central bands of the boxplots represent the median, the boxes of the boxplots represent the interquartile range (between the first and third quartile), and the whiskers represent the minimum and maximum values, up to 1.5 times the interquartile range. Outliers displayed are outside of this range. (H) Z-disc intervals (sarcomere length) of slow skeletal muscle at 3 dpf in smyhc1+/+ (n = 249), smyhc1-/- (n = 278), smyhc1R673H/+ (n = 246), and smyhc1R673H/R673H (n = 252). The central bands of the boxplots represent the median, the boxes of the boxplots represent the interquartile range (between the first and third quartile), and the whiskers represent the minimum and maximum values, up to 1.5 times the interquartile range. Outliers displayed are outside of this range.
(d) DLD1 cells expressing FOXO(A3)-ER were transfected with glutamine synthetase (GS) siRNA or non-template (NT) control siRNA, and stimulated with 4-OHT for 24 h with or without 3-methyladenine (3-MA). Apoptosis was determined by FACS analysis after labelling cells with annexin V (AxV)-phycoerythrin and DAPI. The graph shows relative fold versus control samples, mean ±  s.e.m. (n=3). *P0.05.
D ER/ER substitutions increase Ub chain formation in multiple UBE2S constructs (WT, UBC only, and UBC-UBD fusion), monitored by Coomassie-staining of non-reduced SDS-PAGE gels.
(G) Pictorial representation of Dextran sulfate sodium (DSS; 2%) induced colitis development in mice.
(E) Cartoons summarizing the effects of TRIB1 binding and WD40 domain mutation/deletion on COP1 localization.
H Comparisons of percentages of vHIP-innervated mPFC (PL and IL) neuron subtypes. Mock, n=4 mice; ZIKV, n=7 mice. P= 0.5343 in CaMKIIa, 0.0117 in PV, 0.7491 in CAL, 0.4484 in SST, 0.1519 in other uncharacterized neuron subtypes. Data information: All data were presented as mean ± SEM. *P<0.05, **P<0.01, Two-tailed unpaired t-test unless described otherwise.
(A) A model of the regulation of physiological cell death in EC-committed EBs based on our epistatic analysis and previous known gene interactions.
D T.E.M. ANGPTL4 immunogold labelling were performed in pancreas tissues from the AP, SAP and ANGPTL4-treated models (n = 5, each group).
B) Gene Set Enrichment Analysis (GSEA) identifies Stem-cell like expression signature in KL tumors compared with KrasG12D/+; P53-/- (KP) lung tumors (B). Significance was calculated by permutation test.
Quantification of autophagosomes motility from live cell microscopy (Supplementary Movie 1) from mCherry-LC3B L6 cells under basal, iron (250 µM, 24 h) and starvation (amino acid free) condition. Experiments were performed three times, and one representative experiment is presented here. *P < 0.05 (unpaired Student's t-test compared to Iron 24h).
(D) Macrophages were infected with Mtb-WT, Mtb-Δeis, or Mtb-c-eis in the presence or absence of zVAD-fmk (20 µM) or 3-MA (10 mM). Staurosporine (STS; 500 nM) was used as a positive control. After 36 h, cells were stained with PI and then examined by fluorescence microscopy. Data are presented as the mean±SD of at least three separate experiments, each performed in duplicate. *p<0.05, ***p<0.001, vs. Mtb-WT-infected condition (A and B); Mtb-Δeis-infected condition without inhibitors (D). UI, uninfected.
(C) Heatmap depicting the ecdysone inducibility fold changes caused by individual knockout of motifs in different core promoters. Disrupted INR (highlighted with the black dotted line rectangle) had a slightly negative effect on changing the core promoter responsiveness to ecdysone. (~ 2.3-fold reduction on average, Wilcoxon rank-sum test p = 2.1×10-5). Constitutive and developmental promoters highlighted in red and green, respectively.
(a) Wild-type (WT), atg17Δ, atg7Δ and atg19Δ strains containing RPL25-GFP were grown to mid log phase, starved in SD-N for 48 hours and examined under a fluorescence microscope (left panel). The arrows indicate vacuolar accumulation of the GFP signal. CVT, cytoplasm-to-vacuole-targeting pathway. After the times indicated, at least 100 cells per sample were scored for the presence of Rpl25p-GFP in the vacuole (right panel). Scale bar, 5 μm.
Western blot analysis of nuclear fraction, quantification in G, ratio paired-t-test.
(A, B) Localization of oskar mRNA in wild-type (A) and in Tm1eg9/Tm1eg9 (B) egg-chambers.
Indicated cell lines were plated in serum-proficient (10%) or serum-deficient (1%) media and total cell number counted at 24, 48, and 72 h in biological triplicate.