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Additional file 1: Fig. S1. CrkL binds through the SH3N domain and with similar affinity to the four isolated PRMs of C3G. Fig. S2. Analysis of CrkL by sedimentation velocity. Fig. S3. ITC analysis of the binding of CrkL to single-PRM mutants of C3G. Fig. S4. Linear concentration dependence of the nucleotide exchange activity of phospho-C3G. Fig. S5. Binding of CrkL fragments and CrkII to C3G. Table S1. Constructs of human C3G in the vector pETEV15b-His-Halo-TEV for expression in E coli. Table S2. Oligonucleotides used to create constructs of C3G and for site directed mutagenesis. Table S3. Constructs of human C3G in the vectors for expression in mammalian cells. Table S4. Constructs of human CrkL and CrkII in the vectors for expression in E coli. Table S5. Oligonucleotides used to create constructs of CrkL and CrkII. Table S6. Oligonucleotides to subclone the abGFP4 nanobody in a modified pET22b vector. Table S7. Parameters of the CrkL/C3G interaction determined by ITC. Table S8. Hydrodynamic parameters of C3G and CrkL. Table S9. Parameters of the CrkL/C3G interaction determined by ITC and sedimentation velocity. Table S10. Parameters of the CrkL binding to single-PRM mutants of C3G determined by ITC. Table S11. Parameters of the binding of CrkL fragments to C3G determined by ITC., Universidad de Salamanca Ministerio de Ciencia e Innovación Consejería de Educación, Junta de Castilla y León Agencia Estatal de Investigación National Institute of Biomedical Imaging and Bioengineering Junta de Castilla y León Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Additional file 2. Raw data of the figures., Universidad de Salamanca Ministerio de Ciencia e Innovación Consejería de Educación, Junta de Castilla y León Agencia Estatal de Investigación National Institute of Biomedical Imaging and Bioengineering Junta de Castilla y León Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Supplementary Figure S1. Flp1 phosphatase changes its subcellular localization under oxidative stress in a phosphorylation-dependent manner. (a) Live-cell images of gar2-mCherry cells also expressing either Flp1-GFP, Flp1-6A-GFP or Flp1-9A-GFP fusion proteins under unperturbed growth conditions or after treatment with 1mM of H2O2 for 1 h. Asterisks indicate Flp1-GFP nucleoplasmic localization. Scale bar, 5 µm. (b) Line scans of Flp1-GFP and Gar2-mCherry fluorescence of the boxed nuclei from de merged images in (a), represented by a white line and spanning 4 µm from the white closed circle. Fluorescence intensity was normalized to the maximum value after background subtraction. (c) Schematic representation of Flp1 showing all nine RxxS putative phosphorylation sites, which are mutated to alanine in the Flp1.9A-GFP mutant. Asterisks indicate the six serine residues that are mutated to alanine in the Flp1.6A-GFP mutant. (d) The graph shows the percentage of nuclei with Flp1-GFP, Flp1.6A-GFP or Flp1.9A-GFP detected in the nucleoplasm both under unperturbed growth conditions and after treatment with 1mM of H2O2 for 1h. Supplementary Figure S2. flp1+ deletion partially rescues sensitivity of Dsty1 strain to chronic presence of H2O2 in a pap1+-dependent manner. Tenfold serial dilution of indicated strains were spotted onto YES-agar plates without or with 0.6 mM H2O2 and incubated at 30ºC during 72 h. Supplementary Figure S3. (a) Expression of stress-responsive genes indicated in unstressed wildtype and ∆flp1 cells. Total RNA from asynchronous cultures of the indicated strains grown at 30 ºC was extracted and reverse transcribed using a mix of oligo(dT) and random hexamers primers. mRNA levels of ctt1+, gpd1+, hsp9+ and pyp2+ genes were measured by qPCR and normalized with ribosomal 18S mRNA. The amount of mRNAs relative to the wild-type was expressed as means SD in triplicate. Asterisks indicate statistical significance (*, P<0.05; t-test unpaired) versus wild-type. (b) Exponentially growing cultures of strains indicated at 30 ºC were treated with 1mM H2O2 for 1 hour. Total RNA was extracted, separated by electrophoresis and rRNAs stained with methylene blue were used as loading control. Northern-blot analysis was used to measure the expression levels of atf1+ in the indicated strains. Full-length blots are shown in Supplementary Fig. S9. Supplementary Figure S4. Flp1-9A-GFP strain, expressing a nonphosphorylatable flp1 mutant unable to exit the nucleolus under oxidative stress conditions, shows altered the transcriptional profile of genes such as atf1+, pcr1+, ctt1+, gpd1+ and srx1+ induced in response to oxidative stress. mRNA levels of the mentioned genes were measured by qPCR from total RNA extracted from wild-type and Flp1-9A-GFP strains growing in YES medium containing 1mM H2O2. Total RNAs were prepared from treated cells at the time points indicated. mRNA levels were normalized with ribosomal 18S mRNA and determined with respect to time 0´ value, which was considered as 1. Data represent the average of two biological replicates. Supplementary Figure S5. Dflp1 cells show greater resistance to moderate oxidative stress conditions. Asynchronous cultures of indicated strains growing at 30ºC in YES were incubated with 0.2 mM of H2O2 during 1 h. Then, cells were stressed with 2 mM (a) or 25 mM (b) H2O2. Cell viability was measured at the time points indicated by plating the appropriate dilution of cells onto YES agar plates. The number of viable cells was measured after 3 days incubation at 30ºC. Viability is expressed as a percentage of the number of colonies obtained before the addition of the first dose of H2O2. Supplementary Figure S6. Protein levels of Pyp2 phosphatase upon oxidative stress induction. Wild-type and ∆flp1cells expressing a Pyp2-Myc fusion protein were grown in YES medium to midlog phase and treated with 1mM H2O2 for the indicated times. Total extracts were resolved by SDSPAGE and analyzed by Western blot. Pyp2 was detected by incubation with anti-Myc antibody. Tubulin was used as loading control. Normalization of quantified Pyp2 is shown in bar diagrams. Experiment was repeated three times (Supplementary information Fig. S11), and a representative experiment is shown. Blot membranes were cut prior antibodies incubation. Supplementary Figure S7. Viability of Dpcr1 and Dflp1 Dpcr1 mutants in response to oxidative stress. (a) Tenfold serial dilution of indicated strains were spotted onto YES-agar plates without or with 0.6 mM and 1mM H2O2 and incubated at 30ºC during 72 h. (b) Asynchronous cultures of indicated strains growing at 30ºC in YES were incubated with 2 mM of H2O2 during 1 h. Cell viability was measured before and after treatment by plating the appropriate dilution of cells onto YES agar plates. The number of viable cells was measured after 3 days incubation at 30ºC. Viability is expressed as a percentage of the number of colonies obtained before the addition of H2O2 (0´). Data represent the average of two biological replicates. Supplementary Figure S8. Full-length gels and blots relating to Figure 2b,c are shown. Supplementary Figure S9. Full-length gel and blot relating to Figure S3b are shown. Supplementary Figure S10. Unprocessed original scans and full-length immunoblots relating to Figure 5a,b are shown. Supplementary Figure S11. Unprocessed original scans and full-length blots relating to Figure S6 are shown. Supplementary Figure S12. Full-length immunoblots relating to Figure 6a are shown. Supplementary Figure S13. Unprocessed original scans and full-length immunoblots relating to Figure 7 are shown., Peer reviewed

LEED and Pt 4f core level of the clean and CO-saturated (111), (645), and (312) Pt surfaces; C 1s and O 1s evolution during CO desorption experiments after surface saturation with 10 L CO at the same surfaces; O 1s α-scans at 90 K after a 0.25 and 10 L CO dose, and at 300 K after 50 L O2 dose; and additional details on the W-model., Peer reviewed

The supporting data contains supporting information (SI.pdf), trained models (*.pth), training configuration (nequip_configuration.yaml) to be used with Nequip code (https://github.com/mir-group/nequip), and minimal working example using the models (minimal_working_example.py). Version v2, Peer reviewed

[Introduction]: Monitoring of innate myeloid cells (IMC) is broadly applied in basic and translational research, as well as in diagnostic patient care. Due to their immunophenotypic heterogeneity and biological plasticity, analysis of IMC populations typically requires large panels of markers. Currently, two cytometry-based techniques allow for the simultaneous detection of ≥40 markers: spectral flow cytometry (SFC) and mass cytometry (MC). However, little is known about the comparability of SFC and MC in studying IMC populations., [Methods]: We evaluated the performance of two SFC and MC panels, which contained 21 common markers, for the identification and subsetting of blood IMC populations. Based on unsupervised clustering analysis, we systematically identified 24 leukocyte populations, including 21 IMC subsets, regardless of the cytometry technique., [Results]: Overall, comparable results were observed between the two technologies regarding the relative distribution of these cell populations and the staining resolution of individual markers (Pearson’s ρ=0.99 and 0.55, respectively). However, minor differences were observed between the two techniques regarding intra-measurement variability (median coefficient of variation of 42.5% vs. 68.0% in SFC and MC, respectively; p<0.0001) and reproducibility, which were most likely due to the significantly longer acquisition times (median 16 min vs. 159 min) and lower recovery rates (median 53.1% vs. 26.8%) associated with SFC vs. MC., [Discussion]: Altogether, our results show a good correlation between SFC and MC for the identification, enumeration and characterization of IMC in blood, based on large panels (>20) of antibody reagents., Peer reviewed

(A) CBK1-T743E cdc15-2 (EW1447), (B) lre1Δ cdc15-2 (YMF3857), and (C) fir1Δ cdc15-2 (YMS3792) cells were grown in YPD and arrested in late anaphase by raising the temperature to 37 °C before the addition of rapamycin to half of the culture for 20 min. Subsequently, to allow progression through the cell cycle, cells were released in the absence (−) or presence (+) of rapamycin. Samples were taken at the specified times to determine cell-cycle progression by flow cytometry. FACS graphs can be found in the supplementary FACS file (S1 File)., journal.pbio.3002263.s003.pdf, Peer reviewed

Data is provided in the recent OBIS-ENV-DATA format, and comprises 8913 georeferenced positions associated with 3195 occurrences of 44 marine taxa.-- 3 files, The CETUS dataset contains effort-based occurrence records collected during a cetacean monitoring programme in the Eastern North Atlantic, since 2012, This research was partially funded by the EU FEDER/FEMP and Portuguese Foundation for Science and Technology (FCT) under the Portugal2020 (Lisboa2020, Algarve2020 and MAR2020) Programme through project OBSERVA.PT (MAR-01.04.02-FEAMP-0002), Peer reviewed

11 páginas, 1 tabla, 2 figuras, Peer reviewed

A. Experimental Part: materials, synthesis of gold bipyramids, partial etching of gold bipyramids, and instrumentation; B. Modeling: volume calculation in the geometric inversion model, three-descriptor analysis of bipyramid shapes, and model aspect ratios; C. Simulation of Optical Properties., Peer reviewed