BUSCADOR RECOLECTA

GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for Dictyostelium species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation., This research was funded by the European Research Council under grant 742288 and by The Wellcome Trust under grant 100293/Z/12/Z; European Research Council [742288]., Peer reviewed

Fig. S1. HPLC-DAD chromatogram of major betalains and phenolic compounds in Opuntia stricta var. Dillenii obtained by conventional extraction method at 280, 370, 480, and 535 nm. Numbers correspond to the identified compounds indicated at Supplementary Table S2., Peer reviewed

Fig. S2. HPLC-DAD chromatograms obtained at 280 nm, 370 nm, 480 nm and 535 nm of the obtained extract obtained by PLE using 50% ethanol as green solvent (ethanol/water, 50/50, v/v) and temperature of 25°C (run 10). Numbers correspond to the identified compounds indicated at Supplementary Table S1., Peer reviewed

Table S2. HPLC retention time (Rt), maximum absorption (λmax) and m/z of the identified major bioactive compounds from Opuntia stricta var. Dillenii according to Gómez-López et al. (2021a)., Peer reviewed

Multicellular life forms have evolved many times in our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for the emergence of multicellularity (MC). In this paper, we address the problem of how the first precondition for multicellularity, namely ‘stay together’ might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell–cell adhesion among growing and dividing cells that exploit a localized resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localized portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients., Supplementary images.-- Pseudocode of the model, Peer reviewed

All relevant data are provided in: Lozano-Ojalvo, Daniel; Berin, M. Cecilia (2022), “Allergen recognition by specific effector Th2 cells enables IL-2-dependent activation of regulatory T cell responses in humans”, Mendeley Data, V1, doi: 10.17632/tdxp6b8b64.1, Peer reviewed

Multimedia component 1., Peer reviewed

Supplementary data 1., Peer reviewed

A) Genomic map showing positions of genes and locations of mutations from CRISPR/Cas9 mutagenesis in the 9x-saur mutant based on the TAIR10 Arabidopsis genome annotation. The first sgRNA directed cuts in both SAUR61 and SAUR64 (green arrows), creating a deletion between them (green bar) and leaving behind a hybrid gene with a frameshift at the junction site (symbolized by a green X). The second sgRNA directed cuts in the remaining genes (blue arrows, with lighter blue indicating slight mismatches between the sgRNA and the genome), leading to deletions (blue bars) and/or frameshift mutations (blue X’s). SAUR gene names are abbreviated as S61 etc. SAUR61-SAUR68 are on chromosome 1 and SAUR75 is on chromosome 5. B,C) 5-day-old seedlings grown on 1x MS/1% Suc medium in long days. Scale bar, 1 mm. D) Hypocotyl lengths of seedlings grown for 4d in short days on 0.5x MS medium. n, 27 (wild type), 22 (9x-saur). E) Cotyledon area of seedlings grown on vertically oriented plates for 6d on MS/1% Suc medium. n, 16 (wild type), 22 (9x-saur). Graphs show means ± s.d. No statistical differences were detected between wild-type and 9x-saur mutant measurements by t-test. F) Sequences of guide RNAs used for CRISPR/Cas9-mediated mutagenesis, wild-type genes, and mutant alleles present in the 9x-saur mutant. Underlines indicate PAM motif adjacent to guide RNA target site, and any mismatches to the guide RNA sequence. Uppercase bold letters indicate insertion mutations. All alleles create frameshift mutations except for saur75-1, which has an in-frame deletion of 13 amino acids in the SAUR domain., Peer reviewed

Response surfaces and contour plots of all optimized methods (Figures S1–S3) and GC-QToF-MS chromatogram of the individual soy by-products (Figure S4)., Peer reviewed