EMBO/sd-character-level-ner huggingface dataset:
Figure 9Representative Western blot of total (mCherry and untagged), cytoplasmic TDP-43 and nuclear levels with and without HDAC6 inhibitor. Quantification of total mCherry and total untagged relative to α-tubulin, ratio paired-t-test. Quantification of relative cytoplasmic mCherry TDP-43 on total fraction, ratio paired-t-test. Quantification of total mCherry and total untagged relative to Histone H4, ratio paired-t-test. Quantification of relative nuclear mCherry TDP-43 on total fraction, ratio paired-t-test. Western blot showing untagged TDP-43 (left panel) and phosphorylation state of the untagged allele (right panel) in WT -and MUT-mCherry motor neurons Ratio quantification of normalized pTDP43/normalized TDP-43 (because of almost the same molecular weight two different blots were used), ratio paired-t-test.
Figure 4(A) H/E analysis of control and Ovol2 SSKO skin at the indicated ages. (B, C) Fold difference in HF length (B) and bulb width (C) between control and Ovol2 SSKO mice at the ages of P22-P26 (n=5 pairs) (D) Ki67 immunostaining in control and Ovol2 SSKO skin. K15 stains the bulge/HG cells (E) AE13 immunostaining. Arrows and '*' indicate specific and background signals, respectively (F) RNA expression of the indicated genes normalized to Gapdh in freshly sorted P23-Bu-HFSCs (n=3 pairs) (G) Clonal analysis of control and Ovol2 SSKO Bu-HFSCs. (H, I) Number (H) and average size (I) of Bu-HFSC colonies from (G) (n=3 pairs) (J) Representative images of patch assay results using control and Ovol2 SSKO epidermal cells along with dermal-only control (K) Quantification of number of HFs (n=3 pairs; each biological replicate is an average of 3 injections) (L) K14 immunostaining of skin from the injection site at 3 days after injection. Arrow points to epidermal spheres. (M) Quantification of epidermal sphere diameter (3 independent experiments using 3 pairs of control and Ovol2 SSKO mice) at 3 days after injection
Tat-P4(C5)2, but not Tat-C5, recon into a novel tetrameric state.Figure 3Size exclusion chromatography (SEC) profiles of PICK1 in absence (pink, Absmax = 11.7 ml) and presence of Tat-C5 (purple, Absmax = 11.7 ml) SEC profiles of PICK1 in absence (pink, Absmax = 11.7 ml) and presence of Tat-P4-(C5)2 (blue, Absmax = 10.7 ml) SEC profiles of PICK1 in absence (pink, Absmax = 11.7 ml) and presence of TMR-Tat-P4-(C5)2 (blue (abs280 nm), red (abs544 nm), Absmax=10.7 ml). Representative SEC profiles of PICK1 (40 µM) incubated with increasing concentration of Tat-P4-(C5)2, colors indicate Gaussian fits of respective population, (red) aggregates/Void, (blue) dimeric PICK1, (green) oligomeric PICK1, (orange) unbound Tat-P4-(C5)2. Quantification of abs280 at Evol = 11.7 ml (dimer - blue) and Evol = 10.7 ml (tetramer - green) as a function of concentration (0-10 µM) of Tat-P4-(C5)2. Light blue line indicates tetramer fraction of total PICK1. SDS-PAGE sedimentation assay showing increased amounts of PICK1 in the pellet (P) fraction with increasing concentrations of Tat-P4-(C5)2. PICK1~50kDa, Tat-P4-(C5)2~10kDa. S denotes supernatant fraction. Small angle X-ray scattering (SAXS) derived scattering curves of a concentration range of PICK1 on absolute scale show concentration dependent aggregation. Pair distance distribution function (pddf) of PICK1 in absence of Tat-P4-(C5)2, indicating very large protein complexes present in sample. SAXS derived scattering curves of a concentration range of PICK1 in complex with Tat-P4-(C5)2 on absolute scale show minor concentration dependent aggregation. Pair distance distribution function (pddf) of a concentration range of PICK1 in presence of Tat-P4-(C5)2, indicating a smaller complex than for PICK1 in absence of Tat-P4-(C5)2. Scattering difference (ΔI(q) = I(q)PICK1+Tat-P4-(C5) 2 - I(q)PICK1) between PICK1 in presence and absence of Tat-P4-(C5)2 at indicated concentration shows a clear difference in scattering below 0.1 Å-1. Proposed EOM ensemble for PICK1, in complex with Tat-P4-(C5)2 (not visible in structure) with shading according to model ensemble percentage (10/20/70 %). C-terminal unstructured regions are removed for clarity.
a) Induction of alternative macroautophagy in WT and Atg5−/−, but not Ulk1gt/gt and DKO, erythroid cells.f2(a) Induction of alternative macroautophagy in WT and Atg5−/−, but not Ulk1gt/gt and DKO, erythroid cells. Erythroblasts and reticulocytes from the liver of embryonic mice (E18.5) were incubated with or without STS (1 μM) for 24 h, followed by staining with anti-Lamp2 (red), anti-Ter119 (green) and DAPI (blue). DAPI-positive erythroblasts and DAPI-negative reticulocytes are shown. Lamp2 image and merged image (DAPI, Ter119 and Lamp2) are shown. Scale bar, 1 μm. Large dots for Lamp2 are observed in STS-treated WT and Atg5−/− cells, but not STS-treated Ulk1gt/gt or DKO cells. (b) Representative electron micrographs of EC incubated with or without STS. Erythroid cells were harvested from the liver of embryonic mice (E18.5), incubated with or without STS (1 μM) for 24 h, and analysed by electron microscopy (EM). Scale bar, 1 μm. Insets of WT and Atg5−/− cells show mitophagy (Scale bar, 0.5 μm). Inset of a Ulk1gt/gt cell showing mitochondria that have not been engulfed (Scale bar, 0.5 μm). Arrows point to non-engulfed mitochondria and the arrowheads indicate engulfed mitochondria. (c-e) Quantitative analysis of mitophagy after STS treatment, calculated from EM photos. Population of reticulocytes with mitophagy (c), number of mitochondria per reticulocytes (d) and population of reticulocytes showing macroautophagy (e) were calculated (n>35 cells per mouse). The data are shown as mean±s.d. (n=3). *P0.05 versus value of WT (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA).
Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.Figure 6Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.A. The total distance traveled during a 5 min open field exposure was similar amongst groups (Fmn2-/- placebo, n=9; Fmn2-/- Vorinostat, n=12). Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.. B. The time spent in the center and the corners during a 5 min open field exposure was similar amongst groups (Fmn2-/- placebo, n=9; Fmn2-/- Vorinostat, n=12). Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat. C. The time spent in the open (o) and closed arms (c) or the center region (Ce) of an elevated plus maze was similar amongst groups (Fmn2-/- placebo, n=7; Fmn2-/- Vorinostat, n=10). Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat. D. Freezing behavior during the memory test was significantly increased in the Fmn2-/- Vorinostat group when compared to the placebo group (P = 0,04) (Fmn2-/- placebo, n=8; Fmn2-/- Vorinostat, n=9). Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.. E. Left panel: The escape latency in the water maze test was significantly improved in the Fmn2-/- Vorinostat group when compared to the placebo group (P < 0.0001, F = 4,86; n=10/group). Right panel: Swim speed was not altered amongst groups Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat. F. Mice of the Fmn2-/- Vorinostat group spent significantly more time in the target quadrant (T) compared to the other quadrants (OQ). Please note the values for OQ are presented as average of all 3 other quadrants (P < 0.0001; n=10/group). 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.
Figure 2Analysis design for the identification of differentially processed Alu RNAs between no AD (n=13) and AD (n=11) patients of the CBB cohort using the DESeq2 R package. Statistical significance was estimated using the Wald significance tests within the DESeq2 package. Normalized counts of processed fragments mapping to the right arm of Alu RNAs that are differentially processed (rows) between AD and no AD for each CBB patient (columns) (Dataset EV1). Red corresponds to higher normalized counts of processed Alu RNA fragments. Analysis design for calculation of the Alu RNA processing ratio in CBB patients short-RNA-seq data. Boxplots depict differences in hippocampi of AD and no AD patients regarding SINE Alu RNA processing ratio (left panel) (a p value of 0.05 was considered as threshold for statistical significance with p=0.01 , n=24, unpaired non-directional t-test) and in total Alu RNA levels (right panel) (ns=not significant). In the boxplots, the central band (the line that divides the box into 2 parts) represents the median of the data, the ends of the box shows the upper (Q3) and lower (Q1) quartiles, the extreme line shows Q3+1.5xIQR to Q1-1.5xIQR (the highest and lowest value excluding potential outliers), while dots beyond the extreme line show potential outliers.
a) The gross anatomical views of representative 4% paraformaldehyde-fixed livers and quantification of liver index.f5(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. (b) The haematoxylin and eosin (HE) and CD45 staining of 10-month-old WT and NRBF2 KO mice livers. The NRBF2 KO liver shows mild increase of ductular reaction (yellow arrow) and isolated necrosis (red arrows). The necrotic foci were further confirmed by CD45 staining (black arrow). This is a representative image from four mice per genotype. Scale bar, 50 μm. (c) The number of necrotic foci and ductular reaction scores were recorded under bright-field microscope. At least 10 randomly selected fields (10 × ) from each mouse and four mice per genotype were analysed. (Data are shown as mean±s.e.m., P values are indicated on the figures. Ductular reaction scores, unpaired Student's t-test; necrotic foci, Mann-Whitney U-test, n=4 mice each group). BD, bile duct; CV, central vein; PV, portal vein.
Figure 6A Bar plot showing LOXL1 transcript levels as measured by semi qRT-PCR normalized to 36B4 of scramble and shLOXL1 expressing ILCs cells in vitro. Data represent mean ± SEM (n=3); Student's unpaired t-test, two-tailed. B Scheme describing the experimental approach used to generate shLOXL1 expressing and control ILC xenograft models. ILC:RFP-luc2 cells were transduced with GFP+ sh-scramble or GFP+ shLOXL1 expressing lentiviruses, selected by FACS and injected into the into contralateral 3rd thoracic and the 4th inguinal gland of NSG females. Xenografted mice were monitored for tumor growth by bioluminescence imaging. Radiance-based tumor growth curves (mean ± SE) for the scramble and shLOXL1 MM134 xenografts. For statistical analysis, mixed-effects with spline regression models were used on log10(radiance) curves Likelihood-ratio tests from the ANOVA function in R were used for model comparison, i.e. to check whether the treatment/group covariate is significant. **p<0.01. D Radiance-based tumor growth curves (mean ± SE) for the scramble and SUM44 xenografts. For statistical analysis, mixed-effects with spline regression models were used on log10(radiance) curves Likelihood-ratio tests from the ANOVA function in R were used for model comparison, i.e. to check whether the treatment/group covariate is significant. **p<0.01. E Representative fluorescent stereo-micrographs of glands injected with MM134:RFP-luc2 cells (left, top and bottom) infected with either GFP:sh-scramble (top) or GFP+ shLOXL1 (bottom), n=5 and 3. Scale bar, 1000 μm. F Barplot showing the ratio of GFP/RFP signal from fluorescent stereo-micrographs of glands engrafted with MM134 cells, n=8. Statistical analysis by paired Student t-test, two-tailed. *p < 0.05. G Representative fluorescensce micrographs of GFP:sh-scramble (n=8) and GFP+ shLOXL1 (n=10) MM134 xenografted glands. ILC cells expressing viral transcripts are detected based on GFP expression (green); DAPI nuclear stain (blue). Asterics point to intraductal growth while arrow points to invasive tumor cells. Scale bars, 50 μm. H Representative fluorescent stereo-micrographs of glands engrafted with SUM44:RFPluc2 cells infected with either GFP:sh-scramble (top) or GFP+ shLOXL1, n=6. Scale bar, 1000 μm. I Barplot (mean ± SEM) showing quantification of the ratio GFP/RFP from fluorescent stereo-micrographs of SUM44. Statistical analysis by unpaired Student's t-test, two-tailed, n=7 sh-scramble and n=6 for sh-LOXL1, ****p < 0.0001. J, K Representative photomicrographs of picrosirius red stained histological sections for sh-scramble or sh-LOXL1 MM134 (J) and SUM44 (K) xenografts. Scale bars, 100 μm.
Impaired fear extinction precedes memory decline in Fmn2 mutant mice.Figure 1Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.A. Freezing behavior tested 24h after training was similar in 3-month old APPPS1-21, 5xFAD and Fmn2 -/- mice when compared to corresponding control groups (n = 10/group).E. Freezing behavior was tested 24h after training in 8-month old APPPS1-21, 5xFAD and Fmn2 -/- mice. A significant impairment in associative memory was observed when comparing APPPS1 mice (n=10) to a corresponding control group (n=8; P** < 0,01), when comparing 5xFAD mice (n=10) to a corresponding control group (n=8; P** = 0,01) and when comparing Fmn2 -/- mice (n=10) to corresponding Fmn2 +/+ wild type mice (n=10; P*** < 0,0001). Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.B. Fear extinction in 3-month old APPPS1 mice is similar to a non-transgenic control group (n=9/group). Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.C. Fear extinction in 3-month old 5xFAD mice is similar to a non-transgenic control group (n=9/group). Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.D. Extinction learning in the contextual fear conditioning paradigm is impaired in Fmn2-/- mice (n=9/group; P*** < 0.001, F = 21,77). Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.F. Freezing was analyzed in 3- (n=11), 12- (n=9) and 16- (n=8) month old male wild type mice. A significant impairment (P < 0,0001) was observed in 16-month old animals when compared to either 3- or 12-month old animals. Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.G. Fmn2 expression measured in blood samples via qPCR was reduced in PTSD patients (n=9) when compared to age-matched controls (n=7; P** = 0,0361). Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice.H. Fmn2 mRNA expression is decreased after dexamethasone treatments in human hippocampal progenitor cells (HPCs) during neuronal proliferation (3 days) and differentiation (10 days) ***Padj < 3.27x10-6) Figure 1: Impaired fear extinction precedes memory decline in Fmn2 mutant mice. I. qPCR revealed that Fmn2 expression is decreased (P* = 0,037) in AD patients (n=9) when compared to age-matched controls (n=8). Error bars indicated SEM.
Ionomycin treatment induces mesenchymal gene transcription without repressing epithelial gene transcription Schematic for RNA sequencing after EMT induction for 48h.Figure 3Schematic for RNA sequencing after EMT induction for 48h. Heatmap illustration of EMT related genes in three independent murine PDA cell lines, sequenced in duplicate, treated with DMSO, 2.5μM Ionomycin, or 10ng/ml TGFβ. Scale indicates Z-score. GSEA of ionomycin versus DMSO (Left) or TGFβ versus DMSO (Right) for EMT signatures. NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA. GSEA of ionomycin versus DMSO (Left) or TGFβ versus DMSO (Right) for calcium signatures. NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA. Leading edge plots showing enrichment of C-EMT gene signatures in TGFβ treated cells (Left) or P-EMT gene signatures in ionomycin (IONO) treated cells (Right), based on GSEA. Enrichment scores (ES), NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA.
Figure 4Analysis design for the identification of differentially processed Alu RNAs between AD (n=67) and no AD patients (n=51) of the MAP cohort using the DESeq2 R package. Statistical significance was estimated using the Wald significance tests within the DESeq2 package. As in Figure 2B, normalized counts of processed fragments mapping to the right arm of Alu RNAs that are differentially processed (rows) between AD and no AD for each MAP patient (columns) (Dataset EV2). Red corresponds to higher normalized counts of processed Alu RNA fragments. Analysis design for calculation of the Alu RNA processing ratio in MAP patients' RNA-seq data. Boxplots depict differences in cortex of AD and no AD patients regarding SINE Alu RNA processing ratio (left panel) (a p value of 0.05 was considered as threshold for statistical significance with p<0.001, n=118, unpaired non-directional t-test) and in full length Alu RNAs (p=0.005). Boxplot representation as in subfigure 2D. Boxplots depict full length Alu RNA levels in cortex of AD and no AD patients separated into three age groups. No significant difference observed between the different age groups of either AD or no AD patients or for the comparisons between no AD and AD of each age group (unpaired non-directional t-test, with p<0.05 considered the threshold for statistical significance, n for no AD=19 (below 85), 19 (between 85 to 90), 13 (above 90); n for AD=8 (below 85), 21 (between 85 to 90), 38 (above 90)). Boxplot representation as in subfigure 2D. Boxplots depict differences in SINE Alu RNA processing ratio in cortex of AD and no AD patients separated into three age groups. No significant difference observed between the different age groups of either AD or no AD patients. A p value 0.05 was considered as threshold for statistical significance for the comparisons between no AD and AD of each age group (unpaired non-directional t-test, with p=0.003 for the comparison below 85, and p < 0.001 for the other two comparisons and n numbers as in (E)). Boxplot representation as in subfigure 2D.
Figure 5(A) Purification of hCAP-G and hCAP-G-H subcomplexes: wild type (WT), CAP-G K60D/R848E double mutant (K60D/R848E) and CAP-G R168E mutant (R168E). Purified protein samples were subjected to SDS-PAGE and analyzed by CBB staining. (B) Double-stranded DNA (dsDNA) and single-stranded DNA binding assay of the hCAP-G. 30-bp dsDNA was incubated with no protein (lanes 1) or increasing amounts of WT hCAP-G (WT; lanes 2-4). 30-mer ssDNA was incubated with no protein (lanes 5) or increasing amounts of WT hCAP-G (WT; lanes 6-8). (C) The dsDNA binding assay for the hCAP-G-H subcomplexes. 30-bp dsDNA was incubated with no protein (lanes 1, 5 and 9), increasing amounts of WT hCAP-G-H subcomplex (WT; lanes 2-4), CAP-G K60D/R848E double mutant (K60D/R848E; lanes 6-8) or CAP-G R168E mutant (R168E; lanes 10-12). (D) The ssDNA binding assay for the hCAP-G-H subcomplexes (E) The molecular surface of hCAP-G in complex with hCAP-H. The structural model of hCAP-G is shown in white. hCAP-H is shown as a green ribbon model. Identical and homologous residues between hCAP-G and YCG1 are shown in blue and cyan, respectively. (F) Zoomed-in view of the HEPES-binding site. R168 of hCAP-H interacts with HEPES.
Fig.Figure 4A, Strains were grown over night at 28°C. Mitochondria were stained for 30 min with MitoTracker Red CMOXRos. Microscopy was done with a LSM 900 Airyscan 2 (Zeiss). Pictures were taken in the GFP and the RFP channel and overlaid (merge). B, HoxA-GFP and CitA-GFP (ca. 170 amino acids from the N-terminus of citrate synthase) were expressed over night at 30°C in minimal medium with 2% threonine and 0.2% glucose. Mitochondria were incubated with 100 μg/ml proteinase K (PK) for 20 min on ice. Crude extract (CE), supernatant 1 (S1) containing mitochondria, pellet 1 (P1), supernatant 2 (S2) and pellet 2 (P2) with mitochondria were analyzed by Western Blot using anti GFP antibodies. CitA-GFPc = cytoplasmic form; CitA-GFPi = imported version. C, D Role of the C-terminal anchor in HoxA. Microscopy was done as in A using a fluorescent microscope without the Airyscan technology. C, Expression of GFP-HoxA lacking the C-terminal anchor (∆CTA) in A. alternata. D, Expression of GFP fused to the CTA motif.
Inferred regulator-target coefficient magnitudes are predictive of interactions in published datasets.Figure 4The rankings of observed induction responses (ascending by trise) and predicted regulator relationships (descending by regression coefficient magnitude) were used to predict edges in multiple published networks (Costanzo 2016 and YeastNet v.3). All non-zero ODE regression coefficients were split into two classes, measured (predicted regulators with an induction experiment) and latent (predicted regulators without an induction experiment). A. ROC curves are shown treating interactions, which overlap with the query edges (non-zero regression coefficients), as positives and all other entries as negatives. 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.
Figure 6(A). Design of luciferase reporter vector comprising the let-7 target region of KRAS mRNA (KRAS reporter). (B). Relative luciferase activity of KRAS reporter or Ctrl (empty) reporter in HEK293FT cells infected with lentiviruses expressing tetracycline-inducible TruB1, mt1, mt2, or GFP 5 days after doxycycline treatment. Significance was assessed using 2‐tailed Student's t‐test, < 0.05*. Data information: All experiments were performed in triplicate. Error bars show SD. (C). Protein expression of KRAS. Protein expression was evaluated by Western blotting. Protein was isolated from HEK-293FT cells transfected with GFP, TruB1, mt1, or mt2 (overexpression, left), and TruB1 KD or ctrl (siRNA, right). (D). Relative expression of let-7 families determined by qRT-PCR in HEK-293FT cells with KD of let-7 family members or ctrl (using 2'-O-methylated antisense inhibitor). Significance was assessed using 2‐tailed Student's t‐test, < 0.05*. Data information: All experiments were performed in triplicate. Error bars show SD. (E). Real-time glo assay for HEK293FT cells infected with lentiviruses expressing tetracycline-inducible TruB1 or GFP, 5 days after doxycycline treatment, with or without KD of let-7 family members. GFP: GFP without let-7 KD. WT: overexpression of wild type TruB1 without let-7 KD. WT + let7 KD: WT: overexpression of wild type TruB1 with let-7 KD. GFP + let-7KD: GFP with let-7 KD. Significance was assessed using 2‐tailed Student's t‐test, < 0.05*. (F). Schematic model for TruB1-dependent induction of let-7.