EMBO/sd-character-level-ner huggingface dataset:
Figure 4(A) Olfactory sex preference test in P20 (left panel) and adult (right panel) control and mutant female mice. Half of the mutant females at P20 showed a preference for males, similar to adults of both genotypes, whereas the other half showed an even more pronounced preference for females than their control littermates at P20. One-way ANOVA, Fisher's LSD multiple-comparison test for P20 mice and unpaired t-test for adult mice; n=4 to 6 from at least 3 litters. (B) Time spent sniffing after the introduction of both male and female odors into the cage of control and mutant littermates. One-way ANOVA, Fisher's LSD multiple-comparison test for P20 mice and unpaired t-test for adult mice; n=4 to 6 from at least 3 litters. (C) Representative traces of spontaneous firing in GnRH neurons from control (left, black) and mutant (right, red) animals at week 2 (upper panels) and week 4 (lower panels); lower traces show an enlargement of the upper trace. (D) Average spontaneous firing frequency in GnRH neurons from control and mutant mice at weeks 2, 3 and 4. Individual males and females used for this analysis are represented by blue and grey dots, respectively. Two-way ANOVA, Fisher's LSD multiple-comparison test, n=8 to 14 neurons from at least 3 animals from different litters. Note that individual neurons from male (n=3 to 8) and female mice (n=5 to 8) used for this analysis are represented by blue and grey dots, respectively. (E) Quantification of evoked firing in GnRH neurons from control and mutant mice in response to current steps. Two-way repeated-measures ANOVA, n=10 to 11 neurons from at least 3 mice from different litters.
M18BP1-1161-580 is sufficient for centromere localization in metaphase egg extract A) Representative immunofluorescence images showing localization of Myc-tagged M18BP1-1 truncations schematized in (B) to metaphase sperm centromeres in M18BP1-depleted extract.Figure 1A) Representative immunofluorescence images showing localization of Myc-tagged M18BP1-1 truncations schematized in (B) to metaphase sperm centromeres in M18BP1-depleted extract. Truncations analyzed are indicated on the left, immunolocalized proteins are indicated above. Scale bar, 10 μm. Insets are magnified 3X. B) Schematic of M18BP1-1 truncations used to define the metaphase targeting domain in (A) and (C). C) Quantification of the average Myc intensity at centromeres from (A). Values are normalized to centromeric signal of full-length M18BP1-1. Graph shows the mean ± SEM of at least three experiments. Significance determined by Welch's unpaired two-tailed t-test, * p<0.05, ** p<0.005.
Figure 3(A) CRISPR-targeted bone marrow chimera workflow, showing flow cytometry detection of donor-derived (GFP+), sgRNA-containing (mCherry+) cells. (B) Development of B cell populations in chimeras' bone marrow and spleen from Cd4- or Sh3gl1-targeted HSCs. Percentage of mCherry+ cells at each stage is normalized to initial infection rate of transferred lineage- cells, and shown as mean + SEM. N =11-12 mice. *p=0.0286, ***p<0.0001 using two-way ANOVA. (C) MZ development in mCherry+ B cell compartment. (D) Representative stain of surface CD86 and CD69 on adoptively transferred HEL-specific follicular B cells 24 hours post SRBC-HEL immunization. (E) Quantification of surface CD86 and CD69 mean fluorescence intensity (MFI). Data show mean and SEM from 6 mice across 2 experiments. (F) Fractions of mCherry+ cells in GC, PC, IgG1+ class-switched and follicular B cells at 4-, 8- and 14-days post SRBC-HEL immunization. N = 8-10 mice; data shows mean and SEM. *p<0.05; ***p<0.001; ****p<0.0001 using 2-way ANOVA with multiple comparisons.
Figure 1(A) Confocal live cell imaging of HeLa cells overexpressing GFP-Bax (green) and mitochondria marked with TMRE 100 nM (magenta) show cytosolic GFP-Bax distribution and healthy mitochondria. Lower panels are zoomed images corresponding to the white rectangle in the upper panel and represent the individual and merged channels. Time shows the minutes after apoptosis induction with Staurosporine (STS) 1 µM. Scale bars, 5µm (overview) and 2µm (zooms)(B) HeLa cells shown in A at longer times after STS treatment. Images show sequential GFP-Bax translocation (green), which correlates with mitochondria depolarization (TMRE, magenta). Scale bars, 5 µm(C) HeLa cells overexpressing GFP-Bax mutant (1-2/L-6) (green) and mitochondria marked with TMRE 100 nM (magenta). Images show constitutive GFP-Bax localization to healthy mitochondria without apoptosis induction. Right panels are zoomed images corresponding to the white rectangle in the left panel and represent the individual and overlaid channels. Scale bars, 5µm (overview) and 2 µm (zooms)(D) Standard deviation of the fluorescence intensity of GFP-Bax blue) versus the corrected total cell fluorescence (CTCF) of TMRE (purple) in individual cells (N=4). CTCF= Integrated Density - (Area of selected cell X Mean fluorescence of 3 background readings). Time 0 corresponds to the normalized time when both events cross in each cell. Black line represents the average of the individual cells.
Figure 4(A) The schematic shows the putative conserved miR-499 binding site within the 3' UTR of the Fnip1 gene. (B) Luciferase reporters containing the wild-type Fnip1 3'UTR or Fnip1 3'UTR mutated in the predicted binding site of miR-499 were used in cotransfection studies in HEK293T cells in the presence or absence of plasmid expressing miR-499 (n = 3 independent experiments). *p < 0.0001 (Fnip1 3'UTR); *p = 0.023 (Mutated). (C) RT-qPCR analysis of Fnip1 and Fnip2mRNA levels in the gastrocnemius muscle of the indicated genotypes (n = 5 mice per group). (D) (Top) Fnip1 protein expression in the gastrocnemius muscle from the indicated mice. (Bottom) Quantification of the Fnip1/Tubulin signal ratio (n = 4 mice per group). *p = 0.014.
Figure 2A-B: pDCs were either mock treated or exposed to the SARS-CoV-2 FR2020 early Wuhan-like strain or the SARS-CoV-2 alpha variant B.1.1.7 (0.1 MOI). Supernatants were collected at indicated time points and the production of type I IFNα (A) and CXCL10 (B) was quantified. Data information: Bars represent mean values with standard error of the mean and symbols represent individual pDC donors (n=3-4). Equal symbols represent equal donors Statistical significance was determined using the ratio paired student T test and compared the treated condition with the time point-matched mock condition * C- J: The FR2020 strain was used in subsequent experiments where pDC were either mock treated (mock, grey), exposed to SARS-CoV-2 at 1 MOI (SARS-2, purple), TLR7 (2.5 μg/mL R837, blue) or TLR3 agonist (800 ng/mL poly(I:C), pink). Supernatants were collected after 24 hrs and analyzed for type I IFNα (C), IFNβ (D), type II IFNγ (E), type III IFNλ1 (F), IL-6 (G), IL-8 (H), CXCL10 (I) and TNFα (J) expression by ELISA. Data information: Bars represent mean values with standard error of the mean and symbols represent individual pDC donors (n=3-4). Equal symbols represent equal donors Statistical significance was determined using the ratio paired student T test and compared the treated condition with the time point-matched mock condition *<p0.05, **<p0.01 ***<p0.001. To evaluate the cytokine response to viral titers and exposure duration, pDCs were exposed to increasing viral inoculums (MOI of 0.01, 0.1 and 1) and IFNα2a mRNA expression was quantified at 24 hrs Data information: Bars represent mean values with standard error of the mean and symbols represent individual pDC donors (n=3-4). Equal symbols represent equal donors Statistical significance was determined using the ratio paired student T test and compared the treated condition with the time point-matched mock condition * To evaluate the cytokine response to viral titers and exposure duration, pDCs were exposed to increasing viral inoculums (MOI of 0.01, 0.1 and 1) and IFNα protein secretion at 24, 48, 72 and 96 hrs (L). Graph depicting simple linear regression of IFNα protein with time of exposure (M). Data information: Bars and line represent mean values with standard error of the mean (M) and symbols represent individual pDC donors (n=3-4). Equal symbols represent equal donors Statistical significance was determined using the ratio paired student T test and compared the treated condition with the time point-matched mock condition and simple linear regression *
Figure 1(A) Overview of yeast phospholipid biosynthesis in the endomembrane system and mitochondria, highlighting the enzymes most relevant to this study. Dashed arrows indicate multistep reactions; blue arrows indicate lipid flow into and from mitochondria, with thickness reflecting the estimated flux. CL, cardiolipin; DAG, diacylglycerol; PA, phosphatidic acid; etn-P, phosphoethanolamine; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; PS, phosphatidylserine; SL, sphingolipids. (B) Structures of the abundant phosphatidylethanolamine molecular species 34:2 (sn-1-palmitoleoyl-sn-2-oleoyl-phosphatidylethanolamine), and 34:1 (top: sn-1-palmitoyl-sn-2-oleoyl-phosphatidylethanolamine; bottom: sn-1-stearoyl-sn-2-palmitoleoyl-phosphatidylethanolamine). Molecular species are indicated by the sum of carbon atoms in the acyl chains : sum of double bonds in the acyl chains. The reader should note that MS1 analysis as used in this study does not reveal the identity of the phospholipid acyl chains. Therefore the most probable acyl chain compositions based on cellular acyl chain composition (see forthcoming Figure 4) have been depicted.
Figure 2Single aRGCs in neocortex in organotypic slices of telencephalon of mouse E14.5 Tis21::GFP embryos were microinjected with recombinant Cas9 protein together with gRNA targeting either LacZ (Control, Con) or GFP (gGFP) and with Dextran 10,000-Alexa 555 (Dx-A555), followed by analysis after 24 h of culture.(A) Scheme of the Cas9/gRNA complex microinjection. (B) Daughter cells of single aRGCs microinjected with either Cas9/control gRNA (top) or Cas9/gGFP (bottom) revealed by Dx-A555immunofluorescence (magenta); Cells 1, aRGC daughter; Cells 2, BP daughter. Dashed lines indicate ventricular surface. Images are maximum intensity projections of 20 (Control) and 24 (gGFP) optical sections. Scale bars, 20 µm. (C) Single optical sections of Cells 1 and Cells 2 depicted in (B), showing the effects of Cas9 and control gRNA (top) or gGFP (bottom) on GFP expression (as revealed by immunofluorescence, green). Cells 1 and Cells 2 are indicated by dotted lines; note the presence of GFP immunofluorescence in the daughter cells in control and its absence upon Cas9/gGFP microinjection. Scale bars, 5 µm. (D) Quantification of the proportion of daughter cells (Dx-A555+) of microinjected cells that show GFP expression 24 h after control (Con, white) or gGFP (black) microinjection. Control is set to 100% and the gGFP condition expressed relative to control (39%). Data are the mean of two independent experiments (3 embryos and 1 litter per experiment, total number of daughter cells scored: control 142, gGFP 88); bars indicate the variation of the two individual values from the mean (P<0.05).
The histone-binding activity of Spt5N is dispensable for progression of the Pol II elongation complex through transcription units.Figure 3(A) Experimental procedure, based on the yeast strains YCE281, YCE350 and YCE356. (B) Immunoblot analysis at the indicated times for the samples described in (A). (C) Cells from the end of the experiment described in (A) were fixed and processed for ChIP-Seq, using antibodies specific for phosphorylated Serine 5 in the C-Terminal Domain of the Pol II catalytic subunit Rpb1 (CTD-Ser5P). For each of the three indicated strains, the histograms represent the normalized read density (DNA sequence read count per million reads, or RPM), across a sample gene body. (D) Average of the normalised read density (RPM) for the CTD-Ser5P ChIP-Seq data from two independent experiments, for regions spanning 1kb upstream and downstream of the Transcription Start Site (TSS) of actively transcribed genes across the yeast genome (the analysis focussed on 821 actively transcribed genes, as described in Materials and Methods). (E) For each transcribed gene, an RNA Pol II Traveling ratio was calculated as indicated. (F) Log2 values of the calculated Pol II traveling ratios for each actively transcribed gene were arranged in order from low to high and then plotted against percentile. (G) Principal component analysis of two independent experiments, for the Pol II CTD-Ser5P ChIP-Seq signal across the yeast genome in the three indicated strains.
Interaction with the EJC is required for Btz function in the ovary.Figure 1(A) diagram of the genomic rescue constructs in which wild type Btz (Btz-WT) or Btz with the H215A and D216A mutations (Btz-HD) is C-terminally tagged with GFP and driven by its endogenous regulatory sequences. (B) Co-immunoprecipitation of HA-tagged Btz-WT or Btz-HD with Myc-tagged GFP or eIF4AIII from transfected S2R+ cells using Myc-Trap Magnetic Agarose beads. The upper Western blot is blotted with anti-Myc and the lower with anti-HA. Input samples are shown on the left and immunoprecipitates on the right. Btz-WT co-immunoprecipitates with eIF4AIII, but Btz-HD does not, although the protein is equally stable. The asterisk represents a likely cleavage product of Btz. (C-F) show stage 10 egg chambers stained with anti-Vasa (C-F) or anti-GFP (E', F'). (C) wild type; (D) germline clones homozygous for the null allele btz2; (E) btz2 germline clones rescued with Btz-WT; (F) btz2 germline clones rescued with Btz-HD. Posterior is to the right. Scale bars, 80 μm. Vasa localization to the posterior pole of the oocyte is lost in btz mutants and is rescued by the wild type but not the EJC interaction-defective transgene. Wild-type Btz-GFP, but not the mutant form, is also slightly enriched at the posterior pole.
Figure 6Molecular structure of CEACAM1 (CC1)-N, in which each strand of the IgV structure is coloured differenty. Molecular structure of the β-IgI3 & CC1 N-terminal domain co-complex. Residues that form the β-IgI3-CC1 interface are highlighted. Close-up of the β-IgI3 (light blue) interface with CC1-N (pink), including highlighting of residues important for forming β-IgI3 (blue) & CC1-N (red) interactions. The GFCC′C′′ strands of CC1-N are shown and labelled, whilst the C to D strands of β-IgI3 are shown and labelled. Binding of rCC1-N to dynabeads (DB) coated with β-IgI3 wild type (WT) or mutants. Mutation of β-IgI3 residues 42, 46 and 53 lead to significant changes in CC1-N binding capacity. Binding of β-IgI3 coupled to Streptavidin-PE to DB coated with rCC1-N wildtype or variants. Mutation of CC1-N residues 29, 44, 89, 91 and 95 lead to significant changes in β-IgI3 binding capacity.
Figure 6(A,B) Tumor growth, body weight change and rectal body temperature after daily p.l. treatment with mCD13-AFR, mCD13-AFN-II or combination thereof, in the B16Bl6 model in C57BL/6 mice (A) or RL model in NSG mice (B). Tumor growth is shown as mean TSI, error bars are SEM (n = 5) (upper panel), or as TSI of individual mice (lower panel). (C) Immunohistochemical staining for PECAM-1 (red), cleaved Caspase-3 (green) and DNA (blue) of B16Bl6 tumors after p.l. treatment with 50µg mCD13-AFR and 23.8µg mCD13-AFN-II. Scale bar is 100µm.
Hsc70/DnaJB1 monomerize Hsf1 by cycles of successive entropic pulling.Figure 5A The rate of Hsc70/DnaJB1-mediated dissociation of HSE-DNA bound Hsf1 depends on the number of HR-B proximal Hsc70 binding sites in the Hsf1 trimer. Hsf1wt (wt) and Hsf1∆(202-213) (∆) monomers were mixed in the indicated ratios and heat shocked at 42°C for 10 min to form mixtures of different homo- and heterotrimers as indicated with the cartoons (the red line and the arrow head indicate the Hsc70 binding site). Numbers indicate the relative fraction of the different species. B Moving the Hsc70 binding site away from the trimerization domain reduces the rate of Hsc70/DnaJB1-mediated dissociation of HSE-DNA-bound Hsf1. Hsf1_t10/20/30, region 202-213 moved by 10, 20, or 30 residues towards the C-terminus. C Anti-FLAG antibodies are not able to dissociate HSE-DNA-bound Hsf1. Red lines in the cartoon indicate the Hsc70 binding site; blue lines and arrow head indicate the inserted FLAG epitope DYKDDDDK. Hsf1_i201/211/221, FLAG-epitope inserted after residue 201, 211 or 221. Anti-FLAG antibodies were split in halfmers by incubation with 2 mM DTT Anti-FLAG antibody halfmers bound to FLAG-epitope containing Hsf1 variants. Hsf1wt and FLAG-insertion variants were analyzed by blue-native gel electrophoresis in the absence or presence of DTT-treated anti-FLAG antibodies as indicated and Hsf1 detected by immunoblotting; t-bound, FLAG antibody-bound Hsf1 trimers; m-bound, FLAG antibody bound Hsf1 monomer. E Predicted Hsc70 binding sites in the trimerization domain of Hsf1. Hsp70 score of the trimerization region residues 130-216 of Hsf1wt (black); Hsf1-I190S,I194S, magenta; Hsf1-I202S,L203S,V205S, blue; and Hsf1-I209S,L211S,L213S, green. Values below -5 are considered good Hsc70 binding sites. Above the graph is the trimeric homology model of the trimerization domain residues 130-203 with side chains of hydrophobic and charged residues in space filling representation in atom colors with carbon in black except for Ile190 and Ile194 where carbon is shown in green. Above the model is the corresponding sequence. Positively charged residues, blue; negatively charged residues, red. Lines below the sequence indicate two distinct regions with net charge +1 and +5. F Trimer-to-monomer ratio of freshly purified Hsf1wt and Hsf1-I190S,I194S in the absence of heat shock, determined by gel filtration and BN-Gel G Rate of Hsc70/DnaJB1-mediated dissociation of HSE-DNA bound Hsf1wt and Hsf1-I190S,I194S
Figure 2(A) Top, widefield image showing the localization of CEP164 and PIDD1 at the mature-mother centriole. Bottom: Representative 3D STORM image of the same centriole showing PIDD1 localization. STORM image colors correspond to the Z-depth with red being the closest to the coverslip and blue being the most distant. (B) 3D STORM image of PIDD1 at the mature mother centriole. The overlaid mask represents the inner and outer diameters of the PIDD1 signal. (C) Inner and outer diameter measurements for distal appendage proteins and PIDD1. Measurements in the shaded region were previously reported in (Bowler et al., 2019). Data displayed as box and whisker plots, where the box represents the upper and lower quartile and the whiskers represent the s.d. Scale bars: 1 μm for all wide-field images of centrioles and 500 nm for STORM images. Data acquired across n ≥6 cells. (D) Quantification of the fraction of cells with PIDD1 localized to the mature mother centriole in PLK4Dox cells expressing an sgRNA targeting the indicated genes. A dot displays measurements from each experiment. Experiments were performed in PLK4Dox polyclonal knockout cells. Data acquired across n = 3 biological replicates. Mean ± s.e.m. (E) Schematic depicting the hierarchy of recruitment of distal appendage proteins. (F) Graph showing the relative growth of doxycycline treated PLK4Dox cells that were knocked out for the indicated genes. Each dot displays measurements from a single experiment. Experiments were performed in PLK4Dox monoclonal knockout cells. Data acquired across n ≥ 3 biological replicates. Mean ± s.e.m. (G) Quantification of the fraction of cells with PIDD1 localized at the mature mother centriole. Experiments were performed in PLK4Dox monoclonal knockout cells. Data acquired across n = 3 biological replicates. Mean ± s.e.m.
Alterations in ATG gene expression after phagocytosis of opsonized E.Figure 6Alterations in ATG gene expression after phagocytosis of opsonized E. coli. ATG3 (2.05±0.27), ATG4 (2.20±0.27), ATG5 (2.89±0.42), ATG6 (2.04±0.40), ATG7 (1.98±0.30) and LC3B (2.46±0.39) gene expression (fold) in E. coli‐phagocytosing neutrophils compared with control cells. Dotted line represents mRNA expression levels of control cells. Data are representative of six independent experiments and are presented as mean relative expression±SD Wilcoxon matched‐pairs test, *p<0.05.
Figure 4Planarians were injected with exoc3(RNAi) or with control gfp(RNAi) injections. Organ phenotypes were analyzed on day-38 of the injection protocol. Organ homeostasis was analyzed by staining against specific markers: (A) The structure of the brain/central nervous system (CNS) was analyzed by staining against synapsin (3C11). The cartoon represents the phenotypic change (upper panel). Representative photographs are shown in the lower panel (3 experimental replicates with 2-3 biological replicates per experiment, scale bar: 0.5 mm). Number ratios in the photographs indicate the total number of animals exhibiting the represented phenotype. There was a significant increase in the occurrence of atrophic cephalic ganglia and sensory neuron loss in exoc3(RNAi)-treated planarians vs. controls (cg: cephalic ganglia; sn: sensory neurons). (B) Planarian visual system was analyzed by staining against VC1. Schematic cartoon (upper panel) and representative images (lower panel) are shown (3 experimental replicates with 3 biological replicates per experiment, scale bar: 0.5 mm). Number ratios in the photographs indicate the total number of animals exhibiting the represented phenotype. Arrows point to photosensitive cells (ps); pigmentary cells (pc) and to the optic chiasm (oc).
Figure 5(A) Quantification of luciferase activity in N. benthamiana leaves expressing CRCK3NLuc and MPK4CLuc or MPK6CLuc. Data were collected three days after infiltration. The data are shown as mean ± SD (n=8) with one-way ANOVA analysis and Tukey test (P < 0.01). Different letters indicate significant differences. The experiments were repeated twice with similar results. (B) Phosphorylation of CRCK3G390R by MPK4. MPK4 was immunoprecipitated from wild type or MPK4::MPK4-FLAG. After incubation with [γ-32P] ATP and the immunoprecipitated MPK4-FLAG protein in protein kinase buffer, CRCK3G390R was separated by SDS-PAGE. The autoradiograph of the gel is shown in the top panel, and immunoblot analysis of MPK4-FLAG levels is shown in the bottom panel. Myelin basic protein (MBP) was used as a positive control. This experiment was repeated three times with similar results. (C) Western blot analysis of CRCK3-FLAG proteins in wild type and mpk4-3. Total protein was extracted from two-week-old CRCK3-FLAG transgenic plants in WT and mpk4 background grown on ½ MS medium plates. The protein extracts were treated with or without λ-PMPase phosphatase. The proteins were separated by Phos-tagTM acrylamide gel electrophoresis and CRCK-FLAG proteins were detected by western blot analysis using an anti-FLAG antibody. Similar results were obtained in two independent experiments. pCRCK3, phosphorylated CRCK3-FLAG protein. (D) Western blot analysis of CRCK3-FLAG and CRCK35S-5A-FLAG proteins in transgenic plants of wild type background. Total protein was extracted from two-week-old plants grown on ½ MS medium plates. The protein extracts were treated with or without λ-PMPase phosphatase. The proteins were separated by Phos-tagTM acrylamide gel electrophoresis and the FLAG-tagged proteins were detected by western blot analysis using an anti-FLAG antibody. Similar results were obtained in two independent experiments. 5S-5A stands for a change in five amino acids (S172A, S181A, S188A, S195A, S202A).