EMBO/sd-character-level-ner huggingface dataset:
Immunofluorescent analysis of WT and Myf6-KO primary myotubes cultured in differentiation media for 7 days and stained with MF20 and DAPI. Scale bar=200μm J Quantification of the fusion index between Myf6-KO (n=54 fields of view from n=3 mice) and WT (n=81 fields of view from n=4 mice) 7DM myotubes. Fusion index is calculated as the percentage of myonuclei out of the total number of nuclei per field of view. Two-tailed t-test, error bars = +/- SD
D. Single residue mutants of conserved glycine residues in Rbd2200-251 (G244R and G246R) were tested for Cdc48 binding as in (C). Western blots (B-D) were imaged using chemiluminescence.
The representative FACS plots show the generation of CD31+CD34+ EPCs at day 5 of differentiation upon PLB treatment from day 2.5 to 5.
(I) Anti-γH2AX ChIP analysis at FRA3B, FRA16D and GAPDH genomic loci was performed in U2OS WT and PIF1-KO cells, or PIF1-KO cells expressing PIF1-WT, and E307Q and L319P mutants before and after APH treatment (0.4 μM, 24 hr). Enrichment of γH2AX at FRA3B, FRA16D and GAPDH loci was calculated using ChIP value in WT cells as 1 for normalization. Data information: Error bars represent the standard deviation (SD) of at least three independent experiments. Signiﬁcance of the differences was assayed by Two-tailed non-paired parameters were applied in Student's t-test. The P value is indicated as *P < 0.05, **P < 0.01, ***P < 0.001 and n.s. (not significant) P>0.05.
(A) Quantification of Greatwall, ENSA/ARPP19 and PP1 phosphorylation based on phospho-proteomic data.
E) Survival analyses of Study 2 animals performed as outlined in the Materials and Methods. Statistics: V, G indicate significant differences versus tumor-bearing vehicle-treated and tumor-bearing GTx-024-treated groups, respectively. p=0.0005 for Combo vs. V, p=0.0064 for Combo vs. G, Logrank (Mantel-Cox) test using Bonferroni corrected threshold for multiple comparisons.
C. ST2 cells deficient in TRAF6 reconstituted with TRAF6(WT) or enzymatically inactive TRAF6(C70A) were stimulated for 15 minutes with SF-IL-17 (500 ng/ml), solubilized and IL-17RSC was isolated via consecutive Flag and Strep immunoprecipitation and analyzed by MS. Number of identified peptides (unique + razor) and iBAQ intensities for each protein in two independent experiments are shown.
d. Statistical analysis of the frequency of IFN+Foxp3+ Tregs in the co-cultures in a of n=6 experiments performed.
(C) Presentation of the HLA‐A2‐restricted tyrosinase peptide in EBV‐B1.11 cells transfected with pINCO‐Tyrosinase is not affected by these inhibitors of autophagy.
(c) Dynamic simulation of epiboly based on a single spherical cortex model (SC) considering a gradient of elastic tension from animal to vegetal and a constricting area at the E-YSL (from Movie EV8 - 40 %; 60 %; 80% epiboly). Color-coded mechanical power map normalized values in arbitrary units (positive - red, negative - blue) (left). Flow lines (right). The mechanical power is supplied at the surface and internal vortices and their shift from animal to vegetal are precisely simulated.
HFFs were stimulated with for 24 h with 10U/mL IFNγ or left unstimulated and subsequently infected with RH, Pru or PruΔgra15 parasites for 3 h. The percentage of vacuoles that stained positive for (D) NDP52 (n=3 for RH, n=3 for Pru and n=3 for PruΔgra15), is shown in the left bar diagram. On the right-hand side, a representative fluorescent image is shown for the Toxoplasma Pru strain, which expresses GFP. DNA was stained with Hoechst 33258. Scale bar is 10 µm. The yellow box inside each representative image is shown as inset pictures with magnification.
(C) Left Panel: Quantified fusion of Vero cells infected at MOI 0.01. Right Panel: Representative images of Vero cells 48h post infection, GFP-Split (Green) and Hoechst (Blue).
B The time course of the distance between the geometrical centers of domains a and a′ and the angle among domains b, b′ and a′ from the simulation of pS357-PDI (red) and PDI (black) (Yang et al., 2014).
A, Representative traces of TMRE fluorescence measured by flow cytometry in mock transfected cells and cells overexpressing the bicistronic FUS-R495x or the monocistronic FUS(Ø)-R495x constructs (n=4, minimum of 50 000 live cells per independent replicates). Mean fluorescence intensity of mock transfected cells treated with a decoupling agent, FCCP, is indicated by a grey dotted line.
(e, f) Measurements of blood glucose levels (e) and body weight (f) performed weekly over the time span of the experiment.
(D-F) MARK4 protein expression was determined by histoimmunochemistry in (D-E) a tissue microarray comprising 90 lung tumor and 10 normal lung samples or (F) a home-made tissue microarray comprising 100 matched cases of primary and metastatic tumors. (D-E) The percentage of positivity for MARK4 staining in lung tumors versus normal lung samples (D) or in lung tumors according to their histological subtypes (E) is represented. (F) The percentage of cases with increased, decreased or unchanged levels of MARK4 in metastatic lesions as compared to the corresponding primary tumors is represented.
The number of overlapped peaks (1186) and genes (1085) in two ChIP-seq experiments. Statistical differences were determined using Fisher exact test.
(A) Expression changes of different classes of TEs in Tet3-KD and Tet-TKD. Shown are log2-fold changes of KD embryos compared to control 2-cell embryos of different repetitive elements subdivided in classes of TEs. Indicated p-values were calculated using a paired two-tailed t-test (*** = p < 0.001, **** = p <0.0001, data are represented as medium smoothed violin plots with indicated median and quartiles as dotted lines).
Long-term systemic symptoms of Col-0, visp1-1, visp1-2, rdr6-15, and sgs3-1 plants inoculated with CMV-2blm at 50 dpi. Scale bar = 2 cm.
Fig. 2. Spironolactone is the primary candidate recovered from the co-culture screen.(E) Spironolactone inhibits ERBB4 receptor dimerization. Dose-dependent dimerization of the ERBB4 receptor was analyzed using a split TEV assay encompassing ERBB4-NTEV-tevS-GV and ERBB4-CTEV plasmids transfected into PC12 cells. 10 ng/ml EGFld was applied as Nrg1 stimulus. Fluc, firefly luciferase activity (black lines); Rluc, Renilla luciferase activity (grey lines, indicating toxicity levels); n=6; data are shown as mean, error bars represent SEM. The insets depict IC 50 values in µM.
M. Expression of neural-lineage genes of Ctrl, NDIME-/-, and NDIME-/-+Rs26-NDIME cells at day 5 of neural differentiation.
C. Fe contents of the whole plants of wild-type plants and photoreceptor mutants grown under white light with either Fe-sufficient (20 µM, +Fe) or Fe-deficient (2 µM, -Fe) conditions for 7 d.
qPCR analysis of the expression of CAT2 in the leaves Four independent experiments were conducted. Values are given as mean ± SD, n=4. *p<0.05 by Student's t test.
(B) Time-lapse microscopy of fixed GFP+ co-isogenic S. flexneri wild type and rfaL mutant after adding 10 µM Alexa-Fluor647-hGBP1F and 2 mM GTP. Bacteria bound by hGBP1F at 5 min and hGBP1F-enclosed bacteria after 60 min were quantified. Combined data from three independent experiments are shown as mean ± SEM. Significance was determined by unpaired t-tests, two-tailed. n.s., not significant; ****, P ≤ 0.0001.
(b) Western blot analysis of VAMP2, actin and LC3-II in HeLa cells where VAMP2 was knocked down, as indicated. The cells were starved in Hanks balanced salt solution (HBSS) and treated with Baf A1 as indicated. (SE, short exposure; LE, longer exposure.) Quantification of LC3-II/actin ratio is shown. Data are representative of three independent experiments and shown as mean ±s.d. (*P0.05; NS, not significant, two-tailed t-test).
Representative confocal microscopy analysis of cells loaded with dichlorofluorescein-diacetate converted in dichlorofluorescein (DCF) (pictures on the left); digital enlargements and false-color rendering of details shown as white contoured squares (pictures on the right); histogram on the left, averaged fluorescence intensity/cell ± SEM of n=3 independent biological replicates.
(C) Confocal images of representative eye cryosections immunostained with anti-Ezrin (green) and anti-ZO-1 (red) antibodies from 2-month-old miR-211-/- and WT control mice sacrificed 3h after light on at 10 AM (diurnal condition). Enlarged boxes highlight Ezrin staining in both basal infoldings (BI) and apical extension (AE) of the RPE. At least n = 6 mice per group. Scale bar 10 μm. Data information: (RPE) Retinal Pigment Epithelium; (OS) outer segment; (ONL) outer nuclear layer; (BI) RPE basal infoldings (AE) RPE apical extensions.
(A-D) 2D 1H-15N-HSQC spectra of the TRIM25 RING domain at a concentration of 125 µM (A) and 570 µM (B), the monomeric TRIM32 RINGcore (C) and TRIM32-RING dimer (D).
(A) Immunoblot analysis of extracts of wild type (WT) and USP8 knockout (KO) 293T cells transfected with Flag-caspase-1 together with empty vector or Myc-NS1.
d, Wild-type SAE2::PK cells were grown as in b. After 120 min induction, rapamycin (200 ng ml-1) was added or not and samples were treated as in b.
B) Comparison of the simulations of the kinetic model version 1 and version 2 with the measured metabolite concentrations. Data information: For the measurements, the means for n = 3 biologically independent samples are shown and the error bars represent ± SD.
(C) Reproducibility of RNA-seq experiment. Pairwise Spearman correlation coefficients between RNA levels showed higher correlations among biological replicates than among non-replicates.
(C-E) Visualization of the relatively consistent DF patterns in selected enriched pathways. The DF results are based on metabolic modeling using the human GEM Recon 3D (Brunk et al. 2018), but for clear visualization, the metabolic network graphs are based on the human GEM Recon 1 (Duarte et al. 2007) to reduce the number of metabolites and reactions displayed (Methods). Metabolites are represented by nodes, reactions are represented by directed (hyper) edges, with edge direction corresponding to the consensus reaction direction and edge color corresponding to the consensus DF direction across datasets (Methods). Red and blue colors correspond to increased and decreased fluxes, respectively; grey color corresponds to reactions not showing consistent DF changes across datasets, some of such reactions are not shown to increase clarity. (C) Pyrimidine synthesis. (D) Inositol phosphate metabolism. (E) Fatty acid synthesis. Metabolites are labeled by their names in (C) or IDs in (D,E), with suffixes denoting their cellular compartments: [c] cytosol; [m] mitochondria. The mapping between the IDs and metabolite names in (D,E) is given in Table EV5C.
FRAP analysis of centriole-associated GFP-OFD1. hTERT-RPE cells stably expressing GFP-OFD1 and centrin1-dTomato were transfected with siRNA against myosin VI. After four days, cells were treated with nocodazole (1 hour, 6 μg/ml) and subjected to live-cell imaging. (D) Left: a scheme of the localisation of GFP-OFD1 and the centriole marker centrin1-dTomato. Right: a scheme of photobleaching and recovery of GFP-OFD1 at the centrioles.
HeLadox-YFP-TIARr cells were transfected with control or TIAR siRNAs, and 24h hours later cell were cultured in the abscence or presence of 1 μg/ml doxocycline for 48 hours. The expression of p(S10)-H3, total H3 and TIAR was measured by Westen blot analysis. The graph shows the quantification of p-H3 levels normalized to total H3 (mean ± SD, n = 4). Data information: Statistical significance was determined by unpaired Student's t-test; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
D Metaphase spreads were prepared as in (C), and the frequency of cells with chromosomal breaks was quantified (mean ± SD, n = 3 independent experiments, approximately 30 metaphase spreads were assessed per experiment and condition). E Metaphase spreads were prepared as in (C), and the frequency of cells with scattered chromosomes was quantified (mean ± SD, n = 3). Data information statistical significance was determined by unpaired Student's t-test; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
Representative images from THP-1 ∆GBP1+Tet-mCH-GBP1 cells stably expressing YFP-CASP4C258S. Cells were infected with STm for 2 h. Blue, Nuclei & STm (Hoechst dye); Red, mCH-GBP1; Green, YFP-CASP4C258S. Scale bar, 5 μm.
RBP ranking based on ES cell abilities to self-renewal (determined by colony formation (±LIF) and Oct4 expression) and exit-from-pluripotency (determined by AP staining, EB formation and marker genes expression) in the context of RBP KO. The expression value of Oct4, FGF5, Hand1 and Brachyury was represented as the relative level of these genes compared to their expressions in WT ES cells. The quantitation of other phenotypes, such as colony formation, AP staining and EB formation was manually defined.
(A,B) Live-cell nanoscopy of Mic10-TO cells. Cells expressing COX8A-SNAP were labeled with SNAP-cell SiR and recorded with STED nanoscopy. (A) Cristae architecture in noninduced cells. (B) Cristae architecture after Mic10 re-expression (24 h induction with doxycycline). STED image data were deconvolved.
B. Hierarchical clustering of the phosphorylated sites differentially quantified in wt- and T693A-expressing T47D stimulated or not with FGF10 for 40 or 60 min.. Four clusters for plasma membrane Response (PMR), Acquired Response (AR), Late Response (LR), and T693 Phosphorylation Dependent Response (PDR) are highlighted with black lines and color-coded on the right with blue, medium, or dark blue and yellow, respectively. The intensity of phosphorylated sites is presented on the logarithmic scale with intensity below and above the mean color-coded in blue and red, respectively.
E) Genomic locus showing a representative example of reconstructed TUs. Genomic coordinates are indicated at the top of the panel (kb). From innermost to outermost tracks: terminators predicted on the positive (purple) and negative (orange) DNA strands; coordinates of TUs on the positive (black) and negative (gray) DNA strands; M. florum genes encoded on the positive (blue) and negative (red) DNA strands; position of motif-associated TSSs identified on the positive (green) and negative (red) DNA strands; RNA-seq and 5'-RACE signals observed on the positive and negative DNA strands, colored-coded identically to TUs and identified TSSs, respectively. Illustrated RNA-seq and 5'-RACE signals represent the number of read and read starts observed for a given position, respectively. RNA-seq signal was smoothed using a 5 pixels window (UCSC Genome Browser integrated function). RNA-seq and 5'-RACE peaks above 20,000 reads and 1,000 read starts are cut and marked by fuchsia dots, respectively.
C) GST, GST-Atg19 C-terminus (control), GST-Ykt6∆ac (1-194 aa), GST-SNARE∆ac (142-194 aa), GST-T-peptide, GST-SS-peptide and alanine (A) mutants were purified from E. coli and in vitro phosphorylated with immunoprecipitated Atg1-TAP bound to IgG magnetic beads. One representative experiment out of three is shown.
(B) Representative images of HeLa cells immunostained with S9.6 and nucleolin antibodies after transfection with at least a pool of two siRNAs of each original pool.
B) Western blot analysis of Ub-K48 proteins in the soluble fractions of intestine lysates from mice plus or minus heat shock. C) Quantification of panel B. Each central line and error bar indicate mean +/- SEM of a biological replicates (n=3 biological replicates per group). Data information: * indicates p<0.05, ** indicates p<0.005, and *** indicates p<0.0005 by unpaired two tailed students t-test comparing male and female samples or samples with or without heat shock.
B, C. MTT cytotoxicity assay. (B) HT22 cell line was treated with various concentrations of Nec-1 (0 - 200 μM). Aggregated Aβ(1-42) was used as the positive control for the induction of neural cell death. All data represented the mean ± standard deviation of three independent experiments performed in triplicate.
Endogenous TRIM21 but not TRIM25 still interacted with SAMHD1. RD-SAMHD1-HA cells treated as in (B) were subjected to TRIM21 or TRIM25 IP and IB.
A: SSEA-1+ TNG E-tdT ESCs were cultured for three days in GMEMβ/FCS/LIF and sorted into GFP+/tdThigh (Nanoghigh/Esrrbhigh) or GFP-/tdTlow fractions (Nanoglow/Esrrblow). The purity of the sorted populations (>99.5%) is shown (day 0). After replating in GMEMβ/FCS/LIF, SSEA-1+ cells were analysed daily for Esrrb-tdTomato and Nanog:GFP expression.
B. Accumulation of activated Parkin in MITOL KO cells. WT or MITOL KO HeLa cells stably expressing HA-Parkin were treated with CCCP (10 µM) for 30 h and then performed Duolink in situ proximity ligation (PLA) assay demonstrating the interaction between Parkin and Ubiquitin. Scale bar, 5 μm. Higher magnification images of the boxed regions are shown in the small panel.
(F) Fluorescence of immobilized Venus-tagged SVs imaged with TIRF microscopy. Scale bar, 2 µm.
Superposition of the SARS-CoV-2 Nsp15 NendoU active site with its homologs:SARS-CoV-2 (teal, chain A), SARS-CoV (pink), MERS-CoV (grey).
Histogram showing the CSPs of 15N-labelled CXCL12 amides (~0.1 mM) upon addition of ten-fold excess of DFL. Missing residues are prolines. Elements of secondary structure are depicted on top.
A) HeLa cells transfected with indicated plasmids expressing mouse (m) or human (h) DGKk were analyzed by immunofluorescence confocal microscopy for HA tag (red) and Dapi staining (blue). ∆C1-hDGKk construct bears deletion of phorbol ester C1 domain (328-449).
(F) A375 cells were infected with an IPTG-inducible ZEB1-shRNA. Left panel: Western blot analyses of ZEB1 expression ± IPTG (100µM) treatment for 6 days. Actin was used as a loading control. Right panel: 2 x 106 IPTG-inducible shRNA-Control or shRNA-ZEB1A375 cells were injected subcutaneously into nude mice. When the tumor reached 5 mm in diameter, ZEB1 expression was silenced by adding IPTG (10 mM) into the drinking water for 20 days. The mean tumor volume for 5 mice is represented (± SEM). (Student's t-test).
Giemsa staining of zygotes/ookinetes from in vitro culture. Upper diagrams indicate morphological changes from zygote to ookinete. Black arrow indicates the apical. Scale bar = 5 μm.
A) Representative nuclear spreads of wild-type pachytene and Rec8−/− pachytene-like spermatocytes. Nuclear spreads were immunostained for SYCP3 and ACA. Magnified views are indicated by dashed areas. Schematic representation on magnified chromosomes represents tightly associated sister-AEs (separated for easier representation) in paired wild-type homologs, and the appearance of two distinguishable/separated sister-AEs once REC8-mediated cohesion is lost in Rec8−/− univalents. Bars, 10 μm in spreads and 1 μm on insets.
The individual networks of up-regulated gene were heat mapped typically, on the clusters of "REGULATE_OF_PHOSPHORUS_METABOLIC_PROCESS", and "POSITIVE_REGULATE_OF_PHOSPHORUS_METABOLIC _PROCESS"
(A) Schematic representation of the putative binding sites for miR-3908 and TRIM59.
(N-O). Immunoblots (N) and quantification (O) of p-HSL and ATGL protein in gWAT of male mice after 11 weeks of AKG supplementation (n = 3 per group).
D. Weights of tissues related to energy metabolism in WT and TRPV2KO mice after 8-week HFD treatment.
B) Summary of srd-1 expression pattern. The transcriptional reporter Psrd-1::gfp was detected in both male and hermaphrodite ASI neurons in the head region, and only in male AWA and ADF neurons.
F TET1 and TET2 Western Blot in nuclear lysates from naïve and activated CD4+ T cells and p84 immunoblot as a loading control.
Fluorescence polarization assays were performed by incubating 6-FAM-labeled RNA with WT, hypomethylated (MS023), and arginine methylation-deficient (RK) mutant METTL14. Each point represents the average of three independent replicates and error bars represent standard deviation (SD). The dissociation constant values (Kd) were listed as mean ± SD.
F-H Same as in (C-D) except using antibodies against γH2AX (red) and RIF1 (magenta). (F) Representative images from cells in S-phase (EdU positive; scale bar 5µm). (G) Quantitation of the number of RIF1 foci per nucleus, and (H) mean volume of RIF1 foci (mean ± SEM of >30 cells per condition and cell cycle stage).
D, E, F Upon completion of the chronic feeding study, resting energy expenditure (REE), respiratory quotient (RQ) and locomotor activity of DIO mice treated with MP-10 (30mg/kg) compared to vehicle control were measured in metabolic cage experiments (n = 4 per group). * P = 0.0239 (02:00, RQ), * P = 0.0424 (02:30, RQ), * P = 0.0420 (03:00, RQ), * P = 0.0230 (03:30, RQ), * P = 0.0213 (04:00, RQ), ** P = 0.0116 (00:00, REE), ** P = 0.00823 (00:30, REE), ** P = 0.00969 (01:00, REE), ** P = 0.00274 (01:30, REE), ** P = 0.00323 (02:00, REE), ** P = 0.000441 (02:30, RE), ** P = 0.00390 (03:00, REE), ** P = 0.000211 (03:30, REE), ** P = 0.00216 (04:00, REE) and ** P = 0.0185 (04:30, REE) using unpaired 2-tailed Student's t tests.
(J) number or (K) area of tPH-CynA-KikGR coated macropinocytic vesicles in wild-type AX2 and RacH− cells. T-test was carried out by GraphPad Prism, *P ≤ 0.05, ****P ≤ 0.0001 versus AX2 group; mean ± SEM (n = 20).
Effect of siRNA-mediated downregulation of protein HuR on cellular expression of pro-inflammatory cytokines. In the left panel of F, effect of siRNA treatment on cellular cytokine mRNA levels in LPS-stimulated RAW 264.7 cells is shown. Relative levels measured against 18S rRNA are plotted. The effect of HuR depletion on cellular miR-155 content has been measured and relative values normalized against U6 snRNA are plotted (right panel, F).
(C) Immunofluorescence microscopy. Primary hepatocytes isolated from wild-type mice were challenged with 10 μM sodium arsenite [As (III)] for 12 hrs and then immunostained with anti-p62 and anti-NBR1 antibodies. Each inset is a magnified image. Bars: 20 µm. The number and size of p62-bodies were measured in more than 100 cells. Data are shown as means ± s.e. ***P < 0.001 as determined by Welch's t-test.
C) Metabolic map containing most relevant reactions (blue) and metabolites (black) of E. coli under anaerobic conditions. Dashed arrows indicate (lumped) reactions with several enzymes involved. Allosteric regulations of the respective reactions are marked in red (inhibition) or green (activation). The kinetic model (version 1 and 2) covers almost all of the shown reactions and regulations; a map directly related to the model is shown in Appendix Figure S1. Abbreviations of metabolites and reaction names: Glcex: external glucose (substrate); G6P: d-glucose-6-phos­phate; F6P: d-fructose-6-phosphate; FBP: fructose-1,6-bisphosphate; GAP: d-glyceraldehyde-3-phosphate; DHAP: dihydroxy­acetone phosphate; BPG: 1,3-bisphospho-d-glycerate; 3PG: 3-phosphoglycerate; PEP: phosphoenol-pyruvate; PYR: pyruvate; AcCoA: acetyl coenzyme A; CoA: coenzyme A; AKG: α-ketoglutarate; OAA: oxaloacetate; FUM: fumarate; SUC: succinate; FOR: formate; LAC: lactate; ACE: acetate; ETH: ethanol; ATP: adenosine triphosphate; ADP: adenosine diphosphate; NAD: oxidized nicotin­amide adenine dinucleotide; NADP: oxidized nicotinamide adenine dinucleotide phosphate; NADH: reduced nicotin­amide adenine dinucleotide; NADPH: reduced nicotinamide adenine dinucleotide phosphate; CO2: carbon dioxide; MQH2: mena­quinol; MQH: menaquinone. PTS: phoshotransferase system; PGI: glucose-6-phosphate isomerase; PFK: phospho­fructo­kinase; FBA: fructose-bisphosphate aldolase; TPI: triose-phosphate isomerase; GHD: glyceraldehyde-3-phosphate dehy­dro­genase; PGK: phosphoglycerate kinase; PGM: phosphoglycerate mutase; ENO: enolase; PYK: pyruvate kinase; PFL: pyruvate formate-lyase (also known as formate acteyltransferase); LDH: lactate dehydrogenase; PTA: phosphate acetyltransferase; ACK: acetate kinase; ACDH: acetaldehyde-CoA dehydrogenase; ADH: alcohol dehydrogenase; PCK: phosphoenolpyruvate carboxy­kinase; PPC: phosphoenolpyruvate carboxylase; CS: citrate synthase; ACO: aconitate hydratase A/B; ICDH: isocitrate dehydrogenase; MDH: malate dehydrogenase; FHD: fumarase; FRD: fumarate reductase; NDH: NADH dehydrogenase; ADK: adenylate kinase; NGAM: ATP consumption for non-growth associated maintenance; ATPase: ATP hydrolysis by F1-ATPase in the ATPase strains.