EMBO/sd-character-level-ner huggingface dataset:
Fig.Figure 1a. Seedlings were transferred 5 days after germination (DAG) to medium supplemented with ammonium (grey) or nitrate (red). Root growth rates (RGR in µm/min) were monitored over a 1200 minutes period. Data represent the geometric mean (± standard error, SE) of 3 biological replicates, n=5 (ammonium) and 6 (nitrate) roots. Light and dark periods are indicated as light or dark gray background, respectively. b. On the left, schematic representation of distinct root zones: Meristematic Zone (MZ), Transition Zone (TZ) and Elongation Zone (EZ). On the right, time lapse imaging of cell growth at the TZ. Cells were visualized using the plasma membrane marker (wave line W131Y). Observation of roots started 2 hours after transfer (2 HAT; blue) on ammonium or on nitrate for 135 min (white) and images were recorded every 20 minutes (9 stacks/root/recording). Red and white brackets indicate the length of meristematic and elongating cells at the last measurement point, respectively. Scale bar=30 µm. c and d. Representation and quantification of cell length in epidermal (e) and cortical (c) cell files. Optical, longitudinal sections of 5 DAG old Col-0 roots 12 HAT to ammonium (C) or nitrate (D) supplemented media. The first 20 epidermal (e) and cortex (c) cells (from quiescent center (QC)) are highlighted in grey and in red on ammonium (C), and in blue and green on nitrate (D), respectively. Scale bar=30 µm. Column bars denote the geometric mean of the cell lengths at the respective positions. Lines represent a polynomial regression fit, with calculated slopes between cells 10 and 20 of 3.32639+0.17172 (ammonium, epidermis), 1.22033+0.08754 (ammonium, cortex) and 1.70502+0.09532 (nitrate, epidermis), 0.82342+0.06973 (nitrate, cortex). Data are derived from 3 biological replicates, n=18 roots in each case. e. Graphical representation of the average number of cell divisions along epidermis (ep) and cortex (co) in 5 DAG root tips 12 HAT to ammonium or nitrate supplemented media. Data are derived from 15 and 17 roots. The statistical significance was evaluated with ANOVA at p<0.05. The box chart components are defined as; box (25%-75%), central band (median line), central box (mean) and the range is within 1.5IQR.
Figure 3Figure 3. Archaellum orientation with respect to the cell envelope. (A-D) show tomographic slices through side views of cones. In the bottom row, white lines show the angle of the archaellum with respect to the surface layer, and red dashed lines show the conserved distance from the archaellum at the membrane to the cone. Scale bar 100 nm (applies to A-D). Figure 3. Archaellum orientation with respect to the cell envelope.Schematic in (E) depicts the 44 nm distance from the cone to the basal body in the membrane for archaella at different radial positions along the cone. Since different radial positions on the cone are located at different distances from the membrane (shorter at the tip and longer at the base), this results in a range of archaellar orientations in the cell envelope.
Specific charge-swap variants of the UBE2SHTH increase enzymatic activity and retain Ub linkage specificity.Figure 1A Structural overview of an E2 (green)~Ub (yellow) undergoing a conformational change from the "open" (PDB: 3UGB) to the "closed" (PDB: 4AUQ) state upon E3 binding, resulting in substrate ubiquitination (Dou et al., 2012; Page et al., 2012). B UBE2SHTH (green, PDB: 1ZDN) charged residues (spheres) that were mutated and tested in autoubiquitination assays. C E139R, E143R, and the combination ER/ER mutant substitutions in UBE2S increase the amount of automodification, monitored by the presence of *Ub (* denotes fluorescently labeled protein) and using SDS-PAGE and fluorescent scanning. 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. UBE2S WT and ER/ER form primarily K11-linked Ub chains, determined by quantifying the total detected diGly linkages (left) and calculating the percentage of specific chain topologies (right) using mass spectrometry.
FOXD3 DNA binding domain is essential for regulation of MERVL and 2CLC genes (A) Electrophoretic mobility shift assay (EMSA) with increasing concentrations (0, 30nM, 60nM, 1.Figure 3(A) Electrophoretic mobility shift assay (EMSA) with increasing concentrations (0, 30nM, 60nM, 1.25μM, 2.5μM and 5μM) of recombinant GST-FOXD3, DNA binding mutants GST-FOXD3 M1 and GST- FOXD3 M2 and fixed concentration (50nM) of 5'-Cy5 labelled dsDNA oligonucleotides (35 bp each) representing MERVL and MSR. The experiment was repeated 3 times. (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). (C) Immunofluorescence analysis of MERVL-gag protein in Foxd3 cKO cells, Foxd3 cKO cells over expressing full length FOXD3 or FOXD3 M1 without and with 4-OHT. Nuclei are labelled with DAPI. The percentage of counted cells (~150 cells per experiment) exhibiting immunofluorescence signal is indicated. Scale bar represents 10μm n= 3 biological replicates. (D) RT-qPCR analysis of, 2C genes Zscan4c and Dppa3 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). (E) Immunofluorescence analysis of the ZSCAN4 protein in Foxd3 cKO cells, Foxd3 cKO cells over expressing full length FOXD3 or FOXD3 M1 without and with 4-OHT. Nuclei are labelled with DAPI. The percentage of counted cells (~150 cells per experiment) exhibiting fluorescence signal is indicated. Scale bar represents 10μm n=3 biological replicates.
Mutation-related mitochondrial function in brain.Figure 4Oxygen consumption rate (OCR) was measured in freshly isolated mitochondria from wild-type and mutant mouse cortex. A OCR in brain mitochondria from 19-months mutant mice (black circle) compared with OCR from wild-type mice (white circle). The sequential injection of mitochondrial substrates and inhibitors is indicated by dotted lines Values corresponding to the different respiratory states are shown. Oxygen consumption rate (OCR) was measured in freshly isolated mitochondria from wild-type and mutant mouse cortex. Baseline OCR, effect of age (p<0.0001) and genotype (p<0.05). Oxygen consumption rate (OCR) was measured in freshly isolated mitochondria from wild-type and mutant mouse cortex. C State 3 OCR (after addition of ADP), effect of age (p<0.001) and genotype (p<0.0001). Oxygen consumption rate (OCR) was measured in freshly isolated mitochondria from wild-type and mutant mouse cortex. D State 3 uncoupled OCR (state 3u after addition of FCCP), effect of genotype (p<0.0001) and age-genotype interaction (p<0.0001). E Ratio of mitochondrial complex IV and complex II activities. F ATP levels. G Superoxide anion radicals.
AβOs induce hypothalamic inflammation, eIF2α phosphorylation and impaired insulin signaling.Figure 4Western blot analysis of eIF2α-P levels in the hypothalamus of mice 4 h (A; n = 4 animals/group) or 7 days (B; n = 6 Veh; 5 AβOs) after a single i.c.v. injection of vehicle (Veh) or 10 pmol AβOs. Graphs show densitometric data normalized by total eIF2α levels. *P = 0.0213. Western blot analysis of ATF4 levels in the hypothalamus of mice 4 h after i.c.v. injection of vehicle (Veh) or 10 pmol AβOs; graph shows densitometric data normalized by β-actin (n = 7 Veh; 8 AβOs). #P = 0.0731; Student's t-test. Western blot analysis of hypothalamic phospho-IKKβ levels in the hypothalamus of mice 4 h (C; n = 6 animals/group) or 7 days (D; n = 4 Veh; 5 AβOs) after i.c.v. injection of vehicle or 10 pmol AβOs. Graphs show densitometric data normalized by total IKKβ levels. In (D), *P = 0.0437; in (E), *P = 0.0444; Student's t-test. Western blot analysis of IκBα (F; n = 6 animals/group) and cytoplasmic phospho-p65-NF-κB (G; n = 4 Veh; 5 AβOs) in the hypothalamus of mice 4 h after i.c.v. injection of vehicle or 10 pmol AβOs. Graphs show densitometric data normalized by actin (F) or total NF-κB levels (G). *P = 0.0207. Nuclear NF-κB levels in the hypothalamus 6 h after i.c.v. injection of vehicle or 10 pmol AβOs in mice. Graphs show NF-κB levels normalized by nuclear marker, lamin B (n = 6 animals/group). **P = 0.0024; Student's t-test. IRS-1pSer636 (I; n = 4 animals/group) and pTyr465 (J; n = 6 Veh; 4 AβOs) levels in the hypothalamus 7 days after i.c.v. injection of vehicle or AβOs in mice. Graphs show IRS-1pSer or IRS-1pTyr levels normalized by total IRS-1. In (I), *P = 0.0043; in (J), *P = 0.0275; Student's t-test. Twelve-hour food intake after a single i.c.v. infusion of insulin (200 mU) in mice. Experiment was performed 7 days after i.c.v. injection of vehicle or AβOs (n = 5 PBS; 5 Veh + Insulin; 9 AβOs + Insulin), data are representative of two independent experiments with similar results. ***P < 0.0001, one-way ANOVA followed by Bonferroni post hoc test comparing Veh-Insulin versus PBS groups.
a) Caspases-3, -6, -7, -8 and -9 did not cleave 35S-Atg5.figf3e) Recombinant Atg5 was digested with calpain and the products sequenced by Edman degradation. Calpain cleaved Atg5 at Thr 193. Comparison of Atg5 sequences of different species demonstrates the presence of the same calpain cleavage site in mice. The sequence alignment was perfromed with Clustal W using sequence data obtained from GenBank. The position of the six-amino-acid deletion causing calpain resistance is indicated in red. (d) Following calpain-mediated cleavage of recombinant Atg5 in vitro, the sample was fractionated by preparative reversed-phase HPLC and analysed by mass spectrometry. The exact relative molecular masses for full-length and truncated Atg5 are indicated. e) Recombinant Atg5 was digested with calpain and the products sequenced by Edman degradation. Calpain cleaved Atg5 at Thr 193. Comparison of Atg5 sequences of different species demonstrates the presence of the same calpain cleavage site in mice. The sequence alignment was perfromed with Clustal W using sequence data obtained from GenBank. The position of the six-amino-acid deletion causing calpain resistance is indicated in red. (f) A six-amino-acid deletion surrounding the cleavage site (35S-Atg5Δ191-196) led to a loss of the calpain cleavage fragment. (g) Calpain inhibition by ALLN blocked both cleavage of Bax and Atg5 in spontaneous and Fas receptor-mediated apoptosis of neutrophils. In contrast, Atg6 did not show evidence for cleavage and its levels remained unchanged in this system. Results of 7 h cultures are shown. (h) Atg5 is not cleaved in apoptotic HeLa cells (5 h staurosporine treatment) lacking the small subunit of calpain, which was silenced by using specific siRNA. (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).
Figure 5A Pairwise Pearson correlation coefficient heatmap of transcriptome profiles (RNA-seq) from 2a2iL-, pRH5, and pRH6 cell lines. Each cell of the heatmap shows the pairwise Pearson correlation coefficient heatmap of genes with the largest expression variances in a pair of samples. B Principal component analysis (PCA) of the mean-centered transcriptome profiles. The share of variation captured by each principal component is mentioned in the axis labels. C The volcano plot shows a differential expression between 2a2iL- versus primed hPSCs lines. X-axis shows the log2 fold-change, and the y-axis shows the negative log10 scaled adjusted P-value (Benjamini-Hochberg). Red and blue points represent up-regulated genes in 2a2iL- and primed cells, respectively (absolute log-2 fold-change >1, adjusted P-value <0.05). Gray points indicate non-significant genes between these states. D Integrated analysis of six different naïve-primed datasets. Circular and triangular points in the PCA plot represent naïve and primed samples, respectively. Each color indicates one dataset. Black points represent data generated in this study. Each dataset is indicated by the name of the corresponding author and the year of publication (Dataset EV2). E Integrated analysis of transcriptome profiles of primed and naïve hPSCs, including primary human embryonic cells. Each point represents a biological sample; the colors represent the cell type. Naïve and primed samples are depicted in red and blue, respectively. Samples from pre-implantation embryo are shown in different colors. The number inside each circle indicates the study from which the data is obtained. The study of Tang et al., 2013 demonstrated as empty circle. Large dash circle indicates morula stage of human embryo which is almost in line with our data (small dash circle). All empty points are from dataset (9) Tang 2013. F Functional annotation of 2a2iL- and primed up-regulated genes. The most significant over-represented Gene Ontology (GO) terms and their significance level, along with related genes are presented in each row. Adjusted P<0.05 (adjusted P-value was obtained using the Benjamini and Hochberg correction to determine the false discovery rate with a log2 fold-change >1). G Bar plot showing KEGG signaling pathway analysis of genes significantly up-regulated in 2a2iL-hPSCs (Benjamini-Hochberg adjusted P<0.05 and log2 fold-change >1). X-axis shows
a,b) Bacteria in the spleens of Slamf1−/−Rag1−/− and Rag1−/− BALB/c mice (a) or Slamf1−/− and Slamf1+/+ BALB/c mice (b) 48 h after intraperitoneal injection of virulent S.figf1(a,b) Bacteria in the spleens of Slamf1−/−Rag1−/− and Rag1−/− BALB/c mice (a) or Slamf1−/− and Slamf1+/+ BALB/c mice (b) 48 h after intraperitoneal injection of virulent S. typhimurium 14028s or attenuated S. typhimurium SseB−. CFU, colony-forming units; ND, not detectable. Data are representative of four independent experiments (mean and s.d.). (c-e) Killing of bacteria by peritoneal macrophages from Slamf1+/+ and Slamf1−/− BALB/c mice exposed to S. typhimurium SseB− (c), E. coli F18 (d) or S. aureus (e), assessed by gentamycin assay. Data are representative of five independent experiments (mean and s.d.). (f) Uptake of bacteria by Slamf1+/+ (red solid lines) or Slamf1−/− (black solid lines) BALB/c peritoneal macrophages incubated at 37 °C with E. coli-eGFP or S. typhimurium-eGFP or by Slamf1+/+ macrophages incubated for 60 min at 4 °C with the bacteria (dotted lines). Right, mean fluorescence intensity (MFI). Data are representative of three independent experiments (mean and s.d.).
Sema3C inhibits pathological angiogenesis in an oxygen-induced retinopathy model in mice.Figure 7Scheme of the experiment. C57BL/6N mice pups at P7 with nursing mothers were subjected to hyperoxic conditions leading to vessel obliteration in the central zone of the retina. At P12, mice pups were returned to room air, which induces vessel regrowth but also pathological neovascularization, characterized by pre-retinal neovascular tufts. At P15, mice pups were injected intravitreally with 1 μg control IgG-Fc (left eye) and Sema3C-Fc (right eye). Retinae were analyzed 2 days later after intravitreal injection. RNA scope analyses showed Sema3C and PlexinD1 expression in pre-retinal tufts (OIR model, P19). The retinae were subsequently stained against collagen IV. Sema3CmRNA was detected in peri-endothelial cells. Scale bar: 20 μm. Nrp-1 expression in pre-retinal tufts (OIR model, P17). Abundant expression of Nrp1 in endothelial cells. Pericytes at vascular tufts were immunostained with anti-NG2. Scale bar, 20 μm. H&amp;amp;E staining shows neovascular tufts (arrows). Representative of five retinae per group in two independent experiments. Scale bar, 50 μm. Whole-mount CD31 immunostaining. The white line defines the whole retinal area, and red line outlines the vaso-obliterative zone. Inset image shows large numbers of peri-retinal tufts (i, arrow heads) in control IgG-Fc-treated retinae compared to Sema3C-treated retinae (ii). Scale bar, 500 μm (upper panel) and 100 μm (lower panel).The avascular area is presented as percentage of the whole retinal area (n = 10 retinae in each group; n.s., non-significant using paired Student's t-test).The formation of pre-retinal tufts was quantified in the superficial layer of the retinal vasculature and normalized to whole retinal area (n = 6 retinae in each group; *P = 0.033 using paired Student's t-test).
Figure 2(A) The expression levels of H3K4me3 and H3 in total extracts of wild-type (WT), mog1Δ, set1Δ and spp1Δ strains were analyzed by western blotting using the indicated antibodies. Bar graphs of H3K4me3 levels after H3 normalization show the mean and standard deviations of at least three independent experiments. The P-value was calculated using Student´s t-test (*, P = 0.01-0.05; **, P = 0.001-0.01; ***, P < 0.001) (B) ChIP analysis of H3K4me3 presence at ADH1, PMA1 and YEF3 promoter (P) and 5'ORF in wild-type (WT) or mog1Δ strains relative to total H3. The bar graphs indicate the mean and standard deviation for at least three independent experiments. The significance of the differences was calculated using Student´s t-test (*, P value = 0.01-0.05; **, P value = 0.001-0.01; ***, P < 0.001) (C) MOG1 interacts genetically with the H3 methylases Set1 and Set2. Ten-fold serial dilutions of the indicated strains were spotted on YPD and incubated for 2 days at the indicated temperatures. (D) histone H3K4A and H3K4Amog1Δ strains were compared with their isogenic strains as in (C)
MaMTH-HTS interactome for wt- and F508del-CFTR.Figure 2Annotated MaMTH-HTS interactome for wt- and F508del-CFTR (green, red and blue edges) expanded with known experimental and predicted interactions from IID v 2021-05 (black/gray edges). Interactions observed in MaMTH-HTS to be shared by both wt and F508del CFTR are indicated by blue edges, while those observed with only wt or F508del are indicated by green and red edges, respectively. Node color represents Gene Ontology Biological process. Black square outline and larger node label indicate CFTR interactions overlapping with IID. Node label colouring highlights interactors functionally validated in this work.
Figure 11Scheme illustrating set-up of TDP-43 interactome analysis. Ranked GO enrichment analysis of mutant versus wildtype TDP-43 interactors indicates nuclear depletion of mutant TDP-43. More detailed GO analysis further highlights nuclear depletion of mutant TDP-43 and potential loss-of-function mechanisms. Several axonal transport factors differentially interact with mutant versus wildtype TDP-43. The mutant TDP-43 interactome is depleted for nuclear transport factors and enriched for proteostasis factors, in line with its observed nuclear depletion and cytoplasmic pathological alterations. Scheme illustrating the effect of HDAC6 inhibition on mutant TDP-43 phenotypes. Ranked GO enrichment analysis highlights the effect of HDAC6 inhibition on the mutant TDP-43 interactome, in line with its restored nuclear localization.
Summary of astrogenesis in the DG from development to aging.Figure 7A Schematics depicting the process of DG astrogenesis along postnatal development. The first astrocytes appeared as early as postnatal day 3 from perinatal neural stem cells. From P10 till P14 astrocyte numbers are constantly increasing also by local astrocyte proliferation leading to an outside-in-pattern of astrogenesis. B Schematics showing neurogenesis and astrogenesis in the adult DG. Comparable to neurogenesis, astrogenesis is a dynamic process. Mostly driven by local astrocyte proliferation, astrogenesis is increased upon running wheel stimulus, and diminished upon aging. GZ = granule zone; ML = molecular layer.
Figure 7 Working model of Tau degradation through the Rab35/ESCRT pathway, and its inhibition by glucocorticoids (GC). Rab35 mediates Tau clearance via the endo-lysosomal pathway by recruiting initial ESCRT component Hrs, which recognizes and sorts ubiquitylated Tau into early endosomes for packaging into MVBs. GC suppress transcription of Rab35, which in turn decreases Tau sorting into MVBs and its subsequent degradation by lysosomes, leading to Tau accumulation and related neuronal atrophy.
Chemical synthesis of βHBP Chemical synthesis of βHBP from d-mannose (1): overview.Figure 1Chemical synthesis of βHBP from d-mannose (1): overview
TBK1 phosphorylates HTT in cellular models: (A) Representative western blot of HTT (ab-MAB5492), HTT pS13 (ab-CHDI-90001039-1) and HTT pT3 (ab-CHDI-90001528-1) upon coexpression of HTTex1 16Q eGFP, mutants with S to A substitutions at T3 or S13/S16 or HTTex1 72Q eGFP with TBK1 or TBK1 kinase-dead (KD) for 48 hour in HEK293T cells (the additional high molecular weight HTTex1 and HTT pS13 band is possibly due to the co-occurrence of phosphorylation at both S13 and T3).Figure 2(A) Representative western blot of HTT (ab-MAB5492), HTT pS13 (ab-CHDI-90001039-1) and HTT pT3 (ab-CHDI-90001528-1) upon coexpression of HTTex1 16Q eGFP, mutants with S to A substitutions at T3 or S13/S16 or HTTex1 72Q eGFP with TBK1 or TBK1 kinase-dead (KD) for 48 hour in HEK293T cells (the additional high molecular weight HTTex1 and HTT pS13 band is possibly due to the co-occurrence of phosphorylation at both S13 and T3). (B) Quantification of the fold changes in the HTT pS13 (upper panel) and pT3 (lower panel) ratio to total HTT compared to those of the kinase-dead mutant from the experiments like in A (n=3). (C) Representative western blot of HTT (ab-MAB2166) and HTT pS13 (ab-CHDI-90001039-1) upon coexpression of HTT N543 55Q with the indicated kinase for 24 hour in HEK293T cells. (D) Quantification of HTT pS13 using the Singulex assay (using ab-MW1 as capture and CHDI-90001039 or 2B7 as detection antibodies for pS13 or total HTT) upon coexpression of HTT N543 55Q with the indicated kinase for 24 hour in HEK293T cells from the experiment in C (representative of 3 repeats). (E) Representative western blot of HTT (ab-MAB2166) and HTT pS13 (ab-CHDI-90001039-1) upon coexpression of HTT-FL 48Q or HTT-FL 48Q S13A/S16A with the indicated kinase for 24 hour in HEK293T cells. (F) Quantification of HTT pS13 using the Singulex assay (using ab-MW1 as capture and CHDI-90001039 or 2B7 as detection antibodies for pS13 or total HTT) upon coexpression of HTT-FL 48Q or HTT-FL 48Q S13A/S16A with the indicated kinase for 24 hour in HEK293T cells from the experiments likein E (n=3). (G) Representative western blot of immunoprecipitated (IP) HTT (ab-MAB2166) and HTT pS13 (ab-CHDI-90001039-1) after lentivirus (LV)-mediated overexpression of TBK1 or TBK1 KD for 72 hour in rat primary striatal neuronal cells. (H) Quantification of the fold changes in the HTT pS13 ratio to total HTT compared to those of the kinase-dead mutant from the experiments like in G (n=3).
Fig.Figure 6(A) Flowchart of the study design for the knockdown CREBH in vivo. (B) Hepatic CREBH protein levels 5 weeks after AAV-shCrebh injection. (n=5 for each group). (C) Hepatic Fgf21 mRNA in the WT and L-HRD1 KO mice 5 weeks after AAV-shCrebh injection. (n=5 for each group). (D) Serum FGF21 protein levels in the WT and L-HRD1 KO mice 5 weeks after AAV-shCrebh injection. (n=5 for each group). (E) Body height and tibia length of the WT and L-HRD1 KO mice 5 weeks after AAV-shCrebh injection (n=5 for each group). (F) Hepatic Igf1, Cyp2d9 and Cyp4a12 mRNA in the WT and L-HRD1 KO mice 5 weeks after AAV-shCrebh injection. (n=5 for each group). (G, H) Percentage of the mated and estrus cycle of the WT and L-HRD KO 5 weeks after AAV-shCrebh injection. 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.