BUSCADOR RECOLECTA

ANNEX 1 - Questionnaire on sea turtle bycatch. ANNEX 2 - Content validation., Peer reviewed

Phylogenetic signal based on Blomberg’s K values of repeat cluster contents obtained from the comparative RE2 analysis of Loliinae samples assessed in each of the four Loliinae groups: (A) Loliinae (38 samples, 38 clusters), (B) Broad-leaved (BL) Loliinae (15 samples, 96 clusters), (C) fine-leaved (FL) Loliinae (17 samples, 122 clusters), (D) Schedonorus (16 samples, 167 clusters), using the phylosig option of the phytools R package. Cluster abundance values (number of PE reads) are indicated in Supplementary Table 4. K values close to one indicate phylogenetic signal, values close to zero phylogenetic independence, and values >1 more phylogenetic signal than expected. p-Values based on 1000 randomizations. Significant values are highlighted in bold., The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses., Peer reviewed

The supplemental files include: the description of the methods, figures of the dipole patterns as a function of temperature for periodicities of n=8 and n=14, derivation of the structural order-parameter, and a discussion on the normalization of the helicity., Peer reviewed

The supplementary material provides (1) detailed derivations of formulae used in the main text: of the NS-subhalo encounter rate accounting for subhalo non-rigidity, and of the probabilities of observing neutron stars in certain temperature ranges, (2) brief discussion on tidal effects of neutron stars on subhalo accretion, (3) elaboration on the applicability of previous cosmic ray and paleo-detector limits to our scenario of clumped dark matter, (4) additional information on the sensitivities of and target regions for future telescopes., Peer reviewed

8 pages. -- Table 1. SAXS data collection and processing. -- Figure S1: Binding of nucleotides does not promote significant conformational changes in Apg2 and Apg2C tertiary structure. -- Figure S2: Characterization of the interaction of Apg2ΔC with Hsc70 in the absence of nucleotides by SPR. -- Fig. S3: NMR chemical shift perturbation analysis. -- Fig- S4: Apg2IDR interacts with Hsc70 with 2-fold reduced affinity in the presence of nucleotides., Peer reviewed

20 pages. -- Figure S1. Bifunctional lipid probes and workflow used for in vivo photoaffinity binding studies. -- Figure S2. Photolabeling experiments of non-lipid nanodomain marker (transferrin receptor) and lipid nanodomain marker (Cav-1) with bifunctional lipids and competition experiments between bifunctional analogues and cold lipids in living cells. -- Figure S3. Role of previously described chol-binding motif in IFN-γR2-chol interaction in vivo. -- Figure S4. Physiochemical analysis of IFN-γR2TMD wild type and mutants. -- Figure S5. Validation of the novel chol-binding domain localized within the IFN-γR2TMD. -- Figure S6. Characterization of IFN-γR1 and IFN-γR2 constructs for ID-PRIME and proof of principle. -- Figure S7. Chol binding is required for IFN-γR transmembrane signal activation and PDL1 cell surface exposure in response to IFN-γ stimulation. -- Figure S8. Subcellular localization of candidate chol-binding proteins. -- Supplementary Table 1. Single-and Multi-span motifs found using MOPRO. -- Supplementary Table 2. List of chol-binding protein candidates., Peer reviewed

Supplementary Table 1. Hi-C experimental statistics. Statistics shown separated by replicates (top table) and merged datasets (middle table for valid pairs and bottom table for filtered reads). Supplementary Table 2. Mass-spectrometry analysis of histone H1 peptides after immunoprecipitation with H1 variant specific antibodies., Peer reviewed

FIG. 1. Nuclear modification factor of the B+c meson compared to that of light charged hadrons, and B+, Bs and D0mesons, as a function of the measured transverse momentum. The total uncertainty is shown for the B+c meson, whereasthe statistical (bars) and systematic (filled rectangles) uncertainties are shown for the other hadrons., FIG. 2. Nuclear modification factor of the B+c meson compared to that of the ground and first excited states of charmonia and bottomonia, as a function of the measured transverse momentum. The total uncertainty is shown for the B+c meson, whereas the statistical (bars) and systematic (filled rectangles) uncertainties are shown for the other hadrons., Peer reviewed

Peer reviewed

Details on simulation and systematic uncertainties., Peer reviewed