EMBO/sd-character-level-ner huggingface dataset:
Reaction scheme, enzyme profiling, and reconstitution of the catabolic arginine transamination network operating in nitrogen-fixing bacteroids.Figure 4(A) Schematic representation of the arginine-transamination reaction network than leads from arginine to succinate. Enzymatic reaction steps are indicated by arrows and annotated with corresponding enzyme commission (EC) numbers. Leftward facing dotted arrows represent ureohydrolase, rightward facing dashed arrows decarboxylases, downward-pointing solid arrows aminotransferases, and dashed and dotted arrows dehydrogenase enzyme reaction steps. The names of the metabolites are indicated above their chemical structures according to the following abbreviations: arginine (ARG), ornithine (ORN), 5-guanidino-2-oxo-pentanoate (GOP), agmatine (AGM), 5-amino-oxopentanoate (AOP), putrescine (PUT) , 4-guanidino-butyraldehyde (GBL), 4-aminobutyraldehyde (ABL), 4-guanidinobutanoate (GBA), 4-aminobutanoate (GABA), succinic semialdehyde (SSA), and succinate (SUCC). (B) Heat map representing enzymatic activities participating in the arginine transamination network with relative enzyme activities highlighted as a color map Rows are annotated on the left with the abbreviated names of the substrates and on the right with the corresponding EC numbers. Columns are annotated by corresponding enzyme names. (C) Recombinant enzymes involved in arginine catabolism were combined into a single reaction mixture using arginine and pyruvate as substrates. Substrate (S) consumption into the products (P) succinate and alanine, including their intermediates (I1,I2), was determined along the time series using LC-MS/MS. (D) The relative metabolite abundance along the reaction time-course is highlighted as a color map
Fig.Figure 1A Schematic representation of WT WNV and WNV-poly(A) genomes. WT 3'UTR is represented by the diagram of secondary structure. Three regions are labeled as SL, stem-loop region; DB, dumbbell region; and 3'SL, stem loop region, respectively. B Rescue of WNV-poly(A) virus. A pool of in vitro transcribed recombinant RNAs with different lengths of internal poly(A) tract were electroporated into BHK-21 cells, and the supernatants were blind passaged in BHK-21 cells for three rounds (P1-P3) followed by propagating in Vero cells. IFA detection of E protein using 4G2 antibody at different passages was shown. C Sequence chromatograms of 3'UTR region of P3 WNV-poly(A). Primer-F and Primer-R represent forward and reverse primers, respectively. The primer sequences were described in Materials and methods. D Comparison of growth kinetics between WT WNV and WNV-poly(A) viruses in Vero cells. E RT-PCR spanning the region from C-terminus of NS5 to CS1 region of 3'UTR for P3 pooled WNV-poly(A) and purified viruses. The primer sequences were described in Materials and methods. Two independent experiments in two replicates were conducted and results of a representative experiment were represented. Values represents mean± sd. Data information: Statistical analysis was performed with two-way ANOVA. n.s. no statistical differences. F Plaque morphology of WT WNV and WNV-poly(A) viruses on BHK-21 cells. G SDS-PAGE analysis of purified WT WNV or WNV-poly(A) particles. Bands corresponding to E and Capsid proteins are denoted. H Neutralizing activity of anti-sera against WNV was measured between pooled WNV-poly(A) and WT WNV by PRNT assay. Two independent experiments were performed in duplicate. The data shown are the average values of the duplicate from a representative experiment with standard deviation (error bars). Data information: Statistical analysis was performed with two-way ANOVA. n.s. no statistical differences.
Visualization of the S.Figure 2Figure 2: Visualization of the S. cerevisiae model expanded to account for enzymes. (A) Network with metabolites and enzymes, color-coded to show the location of enzymes (green dots) and metabolites (color-coded by compartment). (B-C) Cumulative distributions of (B) kcat values All distributions were significantly different with p < 0.05 using a non-parametric Wilcoxon Rank-Sum test (Appendix Table S4). (B-C) Cumulative distributions of (C) molecular weights for three different metabolic groups. All distributions were significantly different with p < 0.05 using a non-parametric Wilcoxon Rank-Sum test (Appendix Table S4).
Figure 5A-H Double immunolabeling of SYCP1 (green) and SYCP3 (red) in wild-type (A-D) and Pds5AB cKO (E-H) spread spermatocytes at the indicated stages. I-L Double immunolabeling of HORMAD2 (pseudocolored in white) and SYCP3 (red). Data information: Sex bivalents (XY) are indicated. Scale bar, 10 μm.
Topical P5 treatment induced the anagen hair cycle through AdipoR1 in vivo.Figure 4A Gross morphology of vehicle-, P5-, or minoxidil- treated WT mice. B Hair cycle scores of vehicle-, P5-, or minoxidil- treated WT mice (n = 16 mice / group); Two-way ANOVA with Dunnett's test compared to the control group. C H&E and IF for versican of skin tissue; scale bars: 100 µm. D Anagen induction scores of vehicle-, P5-, or minoxidil- treated WT mice (n = 4 tissues / mice, 4 mice / group); One-way ANOVA with Tukey's test compared to the control group E Gross morphology of vehicle-, or P5- treated Adipoq-/- mice. F Hair cycle scores of vehicle-, or P5- treated Adipoq-/- mice (n = 4 mice / group); Two-way ANOVA. G H&E and IF for versican of skin tissue; scale bars: 100 µm. H Anagen induction scores of vehicle-, or P5- treated Adipoq-/- mice (n = 6 tissues / mice, 4 mice / group); Unpaired t test I Gross morphology of vehicle-, or P5- treated Adipor1-/- mice. J Hair cycle scores of vehicle-, or P5- treated Adipor1-/- mice (n = 5 mice / group); Two-way ANOVA. K. H&E and IF for versican of skin tissue; scale bars: 100 µm. L Anagen induction scores of vehicle-, or P5- treated Adipor1-/-mice (n = 6 tissues / mice, 5 mice / group); Unpaired t test
Figure 3(A). Bar graph shows quantification of lysosomes (LAMP1+) containing PC1 expressed as % of total number of lysosomes (mean +/- SEM) in Saos2 cells mock transfected or transfected with SiRNA against the indicated genes and treated with 100 nM BafA1 for 9h. n=20 cells per condition; three independent experiments. One-way ANOVA (P<0.0001) with Dunnett's multiple comparisons test performed, ***P<0.0001. (B) MEF cell lines lacking the expression of indicated genes were treated for 12h with 50 nM BafA1, fixed and immunolabeled for PC1 (568, red) and LAMP1 (488, green). Scale bar = 10 µm. Insets show magnification of the boxed area. Bar graph (on the left) shows quantification of LAMP1 vesicles positive for PC1, expressed as % of total lysosomes (mean +/- SEM), n=12, 10, 12, 10, 7, 10 cells per genotype respectively; 3 independent experiments. One-way ANOVA with Dunnett's multiple comparisons test performed and P value adjusted for multiple comparisons. ns ≥0.05, *** P<0.0001.
Figure 5H1-T6SS dynamics in tagged parental strain (∆retS TssB1-mCherry2, referred to as WT H1) and ΔtssA1PA strain. Blue arrow indicates extending and contracting T6SS sheath structures, white arrow points to dynamic sheath spots. Scale bars: 2 µm. Fluorescence microscopy of T6SS dynamics in ∆retS TssB1-mCherry2 strain harboring pPSV35 plasmid with TssA1PA-mNeonGreen fusion. Scale bar: 2 µm. Kymographs of TssB1 and TssA1PA dynamics. TssA1PA localizes exclusively at sheath initiation site (B-E), disappears after contraction (C,D) or remains in place for longer timeframe (C,E). TssA1PA signal appears in neighboring cell shortly after T6SS attack (B,C).
Figure 3A-C Live confocal images of ddaC neurons visualized by ppk-Gal4 driven mCD8::GFP expression at WP or 16 h APF. While expression of control RNAi in ddaC neurons (A) did not affect the dendrite morphogenesis nor the pruning processes, knockdown of tacc using RNAi #1 (B) or tacc59/tacc74 transheterozygous mutant (C) severely perturbed the dendrite arborization as well as pruning. Red arrowheads point to the ddaC somas. D Percentages of ddaC neurons showing severing defects in (A-C) at 16 h APF. E Quantitative analysis of unpruned dendrite lengths in (A-C) at 16 h APF. F-H Live confocal images of ddaC neurons visualized by ppk-Gal4 driven mCD8::GFP expression at WP or 16 h APF. Simultaneous knockdown of tacc and msps via co-expressing tacc RNAi and msps RNAi (H) in the ddaC neurons did not enhance the pruning defects, compared to those neurons co-expressing control RNAi and msps RNAi (F). Red arrowheads point to the ddaC somas. I Percentages of ddaC neurons showing severing defects in (F-H) at 16 h APF. J Quantitative analysis of unpruned dendrite lengths in (F-H) at 16 h APF.
Combined pharmacologic inhibition of TOP2A and CCNB1 synergistically inhibits CRPC cell proliferation.Figure 4The CRPC cell line 22Rv1 was cultured in 2% CSS media and was treated for 72 hours with vehicle (DMSO), doxorubicin (DOX), N9-isopropylolomoucine (N-9), or the combination of DOX and N-9 at different concentrations. Cell confluence was monitored using Incucyte Zoom System and the experiments were done with eight replicates each. The data were analyzed using Compusyn software, and a normalized isobologram was built. The table shows the Combination Index (CI) for the different drug combinations. CI=1 represents additivity, CI<1 synergism, and CI>1 antagonistic effects. The non-tumorigenic prostate epithelial cell line RWPE1, the AR-null PC cell line PC3, the androgen dependent cell line LNCaP, and the CRPC cell lines C4-2B and 22Rv1 were treated for 72 hours with vehicle (DMSO), DOX (100 ng/mL [184 nM]), N-9 (200 ng/mL [613 nM]), or the combination of DOX (100 ng/mL [184 nM]) and N-9 (200 ng/mL [613 nM]). C4-2B and 22Rv1 cells were kept in 10% CSS media, and the other cell lines in 10% FBS. Cell confluence was monitored using the Incucyte Zoom System. Data represent two independent experiments, with four to six replicates each, showing the mean ± s.e.m., and normalized to vehicle controls (Kruskal-Wallis test, P value <0.0001, two-tailed). *Significant at a p value < 0.05, ** p value < 0.01, *** p value < 0.001. The non-tumorigenic prostate cell line RWPE-1 and the CRPC cell line 22Rv1 were treated for 72 hours with vehicle (DMSO) or the combination of DOX and N-9 at 100 ng/mL and N-9 200 ng/mL, respectively. Cell confluence was monitored using the Incucyte Zoom System.
Figure 4Figure 4. Modeling BlaM circuit-mediated microbial swarmbot safeguard under a pulsing condition.Left: a periodic pulsing condition. Right: quantification of safeguard effectiveness by evaluating the AUC of the difference between the cell density in the swarmbot and that in the chamber (ΔN). A larger AUC corresponds to more effective safeguard.Effectiveness of safeguard (AUC) as a function of the antibiotic concentration (Ia) and the nutrient concentration (Is). The heatmap is divided into three regions: No safeguard - cells grow both in the swarmbot and in the chamber; Safeguard - cells grow in the swarmbot but not in the chamber; Extinction - cells do not grow in the swarmbot or in the chamber. For each Is, safeguard is achieved for intermediate Ia values. The range of Ia values able to support safeguard is wider for smaller Is values.Sample temporal swarmbot dynamics corresponding to different combinations of Ia and Is values. Panels 1-3 correspond to No safeguard; panels 4-7 correspond to Safeguard; panels 8-9 correspond to Extinction.
RAD54 is dispensable for synapsis at ALT telomeres A Combined IF and DNA FISH for RAD51 (IF) and telomeres (FISH) in SaOS2 or HuO9 cells.Figure 2Combined IF and DNA FISH for RAD51 (IF) and telomeres (FISH) in SaOS2 or HuO9 cells. Cells were transfected with 20nM siRAD54#2 for 48 hours immediately prior to staining. Scale bars = 10 µm Quantification of A. A cell was counted as positive it is contained at least 1 colocalization event between RAD51 and telomeres. At least 100 cells were counted per condition per repeat, n=3. Values shown are mean±sd. Data were compared using standard two-way ANOVA followed by Sidak's multiple comparison test. ChIP for telomeric DNA associated with RAD51. DNA dot blot probed with DIG labeled telomere probe or Alu probe. HuO9 cells were transfected with 20nM siRAD54 #2, or 15µg myc-TRF2 for 72 hours prior to immunoprecipitation with RAD51 antibody (Mock, siRAD54 conditions) or myc antibody (myc-TRF2 positive control). Quantification of (CCCTAA)4 dot blot performed in C. IP values were normalized to loading (IP/input) and then normalized to mock control. Values shown are mean±sd of n=3 biological replicates. Values were compared using two-tailed unpaired student's t-test. Western blot of samples used for ChIP in C-D. Combined IF and DNA FISH for GFP (IF) and telomeres (FISH) in SaOS2 and HuO9 cells. Cells were forward transfected with Polη-GFP, and then after 24 hours transfected with 20nM siRAD54#2. Cells were stained for GFP and telomeres 48 hours after siRNA transfection. Scale bars = 10 µm Quantification of data in F. GFP negative cells were excluded from analysis. Cells were considered positive if they showed 1 or more colocalization events between GFP (Polη) and telomeres. At least 50 GFP positive cells were counted per condition per repeat, n=3. Values shown are mean±sd. Values were compared using standard two-way ANOVA followed by Sidak's multiple comparison test.
Opposite mRNA signatures of Grn-/- / Trem2+/+ and Trem2-/- / Grn+/+ microglia.Figure 1A. Volcano blot representation of the differently expressed genes in FCRLS- and CD11b- positive Grn-/- microglia in comparison to wt microglia isolated from 5.5-month-old mice (male, n = 5). 116 genes out of 529 genes analyzed, are significantly changed, and from these 58 genes are up- and 58 genes are down regulated. Eight genes with the highest fold change are highlighted. B. Heatmap of significantly affected genes (p < 0.05) in FCRLS- and CD11b-positive Grn-/- microglia in comparison to Grn+/+ microglia isolated from 5.5-month-old mice (n = 5 per genotype). For the significantly affected genes of the Grn-/- microglia, mRNA expression data of the Trem2-/- microglia in comparison to the corresponding wt microglia were taken from previously published data (Mazaheri et al, 2017). The RNA counts for each gene and sample were normalized to the mean value of wt followed by a log2 transformation (n ≥ 5 per genotype). * labelled genes were not analyzed or below detection limit in Trem2-/- microglia mRNA expression data set (Mazaheri et al, 2017). C. Changes in gene expression of 359 detected genes in Grn-/- microglia and Trem2-/- microglia. Note that from the 38 genes significantly altered in both genotypes, 32 genes are regulated in opposite direction. D. Gene expression levels of FCRLS- and CD11b-positive Grn-/- microglia normalized to wt in comparison to the published normalized data set of Trem2-/- microglia (Mazaheri et al, 2017).
Surface Mpl is rapidly internalized after Tpo addition, followed by recovery from recycling and autolysosome compartments.Figure 7A) Western blot analysis and quantification of streptavidin‐immunoprecipitated surface‐biotinylated proteins, probed with an anti‐Mpl antibody B and C) Confocal images of K562 cells transiently expressing MplmOrange2. Cells in (B) are untreated. Cells in (C) were stimulated 60' with Tpo, washed and chased for 15 min before imaging. D) Quantification of plasma membrane fluorescence in resting and Tpo‐stimulated cells. Mean fluorescence at the membrane was estimated by averaging the total fluorescence after values equal to or below background. A two‐tailed Student t‐test shows a significant difference in the membrane fluorescence after stimulation with Tpo followed by Tpo removal. Scale bars = 5 µm. E) Western blot analysis of protein phosphorylation in HEL, K562Mpl‐mKO2 and K562Mpl‐mOrange2 cells after Tpo stimulation (50 ng/mL Tpo, 10 min).
Figure 1(A) Representative kymographs showing tetramethylrhodamine (TMR)-labeled DDB movement on each type of recombinant MT lattice, as indicated. Scale bars, 5 μm and 25 sec. Pink arrowhead marks a diffusive DDB complex. See also Movie EV1. (B) Quantification of DDB velocity on MT lattices lacking each of the tubulin-CTTs (n ≥ 100 DDB complexes per condition from at least three independent experiments). No statistical difference was observed between WT and mutant MTs (P ≥ 0.1, unpaired t test) (C-D) Quantification of the number of processive (C), or diffusive (D) DDB complexes relative to WT MTs in the same chamber (n ≥ 10 MTs quantified for each condition from at least three independent experiments). Processive (unidirectional motion exceeding 0.5 μm) and diffusive (back-and-forth motion) events were scored in a field of view and then divided by the lengths of MTs and time, thus normalizing to a value of number of motility events per μm MT per sec. Error bars SD. (E-F) TIRF images of 1 nM TMR-labeled GST-hDyn (2 mM ATP) (E), or 0.3 nM TMR-labeled p150 (F) molecules (green) bound to either Δα-CTT (top), or Δβ-CTT MTs (bottom). Pink arrows show mutant MTs in both the raw, and SD map images, highlighting differences in binding between WT and mutant MTs that are apparent in the SD map. Right, standard deviation maps from an entire time sequence reveal ensemble binding and dissociation events that lead to variations in pixel intensities (see Methods). Scale bars are 5 μm. (G) Quantification of mean fluorescence intensity (arbitrary units) per μm MT for GST-hDyn (2 mM ATP) or p150 bound to the indicated mutant MT relative to WT MTs in the same chamber. Image shows first frame from time series. The intensity of GST-hDyn was quantified from maximum intensity projections of the entire time sequence due to transient binding of GST-hDyn to the MT (n ≥ 10 MTs quantified for each condition from at least three independent experiments). Error bars represent SD. P value (unpaired t test) of Δα-CTT vs. Δβ-CTT MTs = 0.5208 for GST-hDyn, and ≤ 0.0001 for p150.
Figure 7Developmental phenotypes of rosette leaves of 5-week-old Col-0, visp1-1, visp1-2, VISP1OE1, VISP1OE2, and sgs3-1 seedlings. Arrowheads indicate the 8th and 9th rosette leaves from the top leaves. Scale bar = 2 cm.   The length/width ratios of the 8th and 9th rosette leaves of the seedlings shown in A. Every dot represents data from the length/width ratio of one leave (n = 20). Letters indicate significant   differences (ANOVA, P < 0.05). Northern blotting detecting accumulation of TAS1-TasiR255, TAS2-TasiR1511, TAS3-TasiR5′D8, miR173, and miR390 in leaves of Arabidopsis plants shown in panel A. Values represent relative accumulation (RA) of siRNAs and values in Col-0 plants were set as 1. rRNA served as loading controls. RT-qPCR analyzing accumulation of TAS-tasiRNA targets in rosette leaves of 4-week-old Arabidopsis plants. Values in Col-0 plants were set as 1. Data points represent means from three biological repeats. Error bars indicate SD. Letters indicate significant differences (ANOVA, P < 0.05). PPR, pentatricopeptide repeat (PPR); ARF3, auxin response factor 3. Model of VISP1-mediate autophagic degradation of SGS3/RDR6-bodies in Arabidopsis. SGS3/RDR6-bodies mediate dsRNA synthesis for siRNA amplification. Virus infection induce overexpression of VISP1 and selective autophagy. VISP1, a cargo receptor, interacts with SGS3 via the VISP1 Arginine/lysine-rich motif (ARM), and recruits SGS3/RDR6 bodies to ATG8-PE docking site through the VISP1 ubiquitin-interacting motif (UIM). This then promotes selective autophagic degradation of SGS3/RDR6-bodies and negatively regulates amplification of vsiRNAs and tasiRNA.
Figure 2A Pan-neuronal driver elav-Gal4 was used to co-express GFP-Msps and TACC in postmitotic neurons. elav-Gal4 driven mCD8::GFP expression was used as a control. TACC was pulled down by GFP-Msps but not by mCD8::GFP. Alpha-tubulin was used as a loading and probing control. Neither mCD8::GFP nor GFP-Msps could pull down alpha-tubulin. B Endogenous Msps proteins were co-immunoprecipitated with Venus-TACC by GFP beads but not by control IgG beads. Alpha-tubulin was used as loading and probing control. C Endogenous Msps or TACC was pulled down by their respective antibodies, and the other protein was simultaneously detected in the immunoprecipitated contents. Alpha-tubulin was used as loading and probing control. D-G Confocal images of ddaC neurons expressing control RNAi (D), msps RNAi (E), tacc RNAi (F) and αTub84B RNAi (G) that were immunostained for TACC at wL3 stage. ddaC somas are labeled by dashed lines. ddaC neurons are identified by ppk-Gal4 driven mCD8::GFP (green channel) expression, as shown at the top right corner. H Quantitative analysis of normalized TACC fluorescence intensity in ddaC somas. I-L Confocal images of ddaC neurons expressing control RNAi (I), msps RNAi (J), tacc RNAi (K) and αTub84B RNAi (L) that were immunostained for Msps at wL3 stage. ddaC somas are labeled by dashed lines. ddaC neurons are identified by ppk-Gal4 driven mCD8::GFP (green channel) expression, as shown at the top right corner. M Quantitative analysis of normalized Msps fluorescence intensity in ddaC somas. N, O Protein expression of Msps and TACC in brain tissues. (N) Larval brains of msps810/mspsP transheterozygotes at early wL3 stage were immunoblotted and probed with α-Msps and α-TACC antibody. Actin blotting was used as loading control. The dot plot on the right depicts the quantitative analysis of total TACC levels in control and msps transheterozygous larvae. O Protein expression of Msps and TACC in brain tissues. (O) Adult brains of tacc59/ tacc74 transheterozygotes were immunoblotted and probed with α-Msps and α-TACC antibody. Actin blotting was used as loading and probing control. The dot plot on the right displays the quantitative analysis of total Msps level in control and tacc transheterozygotes.
Figure 7(A) Western blotting for Islr in the supernatant from primary cultured intestinal epithelial cells (IECs) transfected with pcDNA3.1 or pcDNA3.1-mIslr-HA plasmids, and western blotting for pMst1/2, Mst1, pMob1 and Mob1, pYap1 and Yap1 in lysates from primary IECs cultured in the supernatants with or without mIslr-HA. β-actin was used as a loading control. (B) Western blotting for Yap1 in nuclear or cytoplasmic proteins from primary intestinal epithelial cells cultured in the supernatant with or without mIslr. Histone H3, a positive control for nuclear proteins. α-Tubulin, a positive control for cytoplasmic proteins. (C) qRT-PCR for Ctgf, Cry61 and Fstl1 in primary intestinal epithelial cells cultured in the supernatant with or without mIslr for 24 hours. n=4. (D) Activity of TEAD-Luciferase reporter in primary intestinal epithelial cells upon mIslr, Yap1 or mIslr and Yap1. n=4. (E) The growth curve of primary intestinal epithelial cells upon mIslr or/and Yap1 siRNA over time. n=5. (F) qRT-PCR for Ctgf and Cry61 in primary intestinal epithelial cells 48 hours after treatments of mIslr or/and Yap1 siRNA (siYap1). n=4. (G) Representative images of primary intestinal organoids cultured at indicated conditions and timepoints. Scale bar: 100 μm. The organoids were co-cultured in a mixed medium of the supernatant with/without mIslr from CT26 cells and regular organoid culture solution at the ratio of 1:4. Quantification of organoids diameter at indicated timepoints. n>150 organoids at each timepoint. (H) Western blotting for pMst1/2, Mst1, pMob1 and Mob1, pYap1 and Yap1 24 hours after the treatment. β-actin was used as a loading control. (I) qRT-PCR for Ctgf, Cry61 and Fstl1 in primary intestinal organoids 24 hours after the treatments. n=3. (J) Immunofluorescence for Yap1 and β-catenin in intestinal organoids 24 hours after the indicated treatments. The treatments are identical to (G). The percentage of nuclear Yap1+ cells versus epithelial cells was quantified. Scale bar: 50 μm. n=12.