BUSCADOR RECOLECTA

Supplementary Material, Appendix 1., Peer reviewed

Table S1. Number of individuals sampled according to species, age and sex. Table S2. Capture systems used for sampling each species included in our active monitoring study to assess avian scavenger exposure to anticoagulant rodenticides in NE Spain. Table S3. MS/MS dMRM transition parameters, recovery and limits of quantification (LOQ) for the analysed SGARs and the internal standard (IS). Table S4. Prevalence (%) and concentrations (ng mL-1)1 of the ΣSGARs concentration > LOQ (i.e., considering only individuals with SGAR levels > LOQ) in the blood of free-living obligate and facultative avian scavengers from the northwest Iberian Peninsula according to age class (nestling, juvenile, subadult and adult). Fig. S1. Percentage of birds containing residues of more than one SGARs in the blood. Regarding SGAR-positive birds (n = 102), we found more than one compound in 48 (47.1%) of the birds. Of these, 31 birds (64.6%) presented with two different compounds; 16 (33.3%) presented with three compounds and one bird (2.1%) presented with four different SGARs. Of all SGAR-positive birds showing more than one SGAR in the blood, 81.2% were Egyptian vultures (n = 25; 58.14% of all), red kites (n = 10; 40%) and black kites (n = 4; 50%). BF (Brodifacoum), DF (Difenacoum), FL (Flocoumafen), BM (Bromadiolone)., Peer reviewed

Supplementary Table S5: Important features identified by One-way ANOVA and post-hoc analysis (Fisher’s LSD) comparing the expression of immune genes in the IMMETCOLS Clusters., Existing immune signatures and tumor mutational burden have only modest predictive capacity for the efficacy of immune check point inhibitors. In this study, we developed an immune-metabolic signature suitable for personalized ICI therapies. A classifier using an immune-metabolic signature (IMMETCOLS) was developed on a training set of 77 metastatic colorectal cancer (mCRC) samples and validated on 4,200 tumors from the TCGA database belonging to 11 types. Here, we reveal that the IMMETCOLS signature classifies tumors into three distinct immune-metabolic clusters. Cluster 1 displays markers of enhanced glycolisis, hexosamine byosinthesis and epithelial-to-mesenchymal transition. On multivariate analysis, cluster 1 tumors were enriched in pro-immune signature but not in immunophenoscore and were associated with the poorest median survival. Its predicted tumor metabolic features suggest an acidic-lactate-rich tumor microenvironment (TME) geared to an immunosuppressive setting, enriched in fibroblasts. Cluster 2 displays features of gluconeogenesis ability, which is needed for glucose-independent survival and preferential use of alternative carbon sources, including glutamine and lipid uptake/β-oxidation. Its metabolic features suggest a hypoxic and hypoglycemic TME, associated with poor tumor-associated antigen presentation. Finally, cluster 3 is highly glycolytic but also has a solid mitochondrial function, with concomitant upregulation of glutamine and essential amino acid transporters and the pentose phosphate pathway leading to glucose exhaustion in the TME and immunosuppression. Together, these findings suggest that the IMMETCOLS signature provides a classifier of tumors from diverse origins, yielding three clusters with distinct immune-metabolic profiles, representing a new predictive tool for patient selection for specific immune-metabolic therapeutic approaches., Peer reviewed

6 pages. -- Supplementary Table S1.Results of the 3-way PERMANOVA for isotopes (δ13C and δ15N), C and N content and C/N ratio in the mussel Mytilus galloprovincialis for the monitoring experiment. -- Supplementary Table S2. Average and standard deviation in δ13C, δ15N, carbon and nitrogen content and C/N ratio of pooled mussels’ tissues of Mytilus galloprovincialis infected and uninfected with the African pea crab Afropinnotheres monodi. -- Supplementary Table S3. Results of the 3-way (Model 2) and 1-way (Model 3) PERMANOVA for isotopes (δ13C and δ15N), C and N content and C/N ratio in the mussel Mytilus galloprovincialis for the monitoring experiment. -- Supplementary Table S4. Average and standard deviation in δ13C, δ15N, carbon and nitrogen content and C/N ratio of pooled mussels’ tissues of Mytilus galloprovincialis and the African pea crab Afropinnotheres monodi after 30 days reared under ad libitum food (Day 30) and subsequently exposed to no access to food during 21 days (Day 51). -- Supplementary text: Isotopic variability of the symbiont and the host species. -- Supplementary Figure S1. Relationships between the carbon and nitrogen isotopic signal (‰) of Afropinnotheres monodi and the muscle of the host bivalve species Mytilus galloprovincialis (locations 2 and 3) and Scrobicularia plana (location 1) in the three locations studied., Peer reviewed

13 pages. -- This PDF file includes: Figures S1 to S7 and Tables S1 to S2. -- Fig. S1. Characterization of scFab-apoferritin fusions. -- Fig. S2. Multabody affinity-purification scheme. Protein A and Protein L sequential affinity purification. -- Fig. S3. Generation of a Multabody that cross-targets the HIV-1 Env and the CD4 receptor. -- Fig. S4. Biophysical characterization of HIV-1 Multabodies. Comparison of the Tm and Tagg temperatures of T-01/T-02 MB, 12-mer ferritin fusions, parental IgGs and the N6/PGDM1400x10E8v4 trispecific antibody. -- Fig. S5. Binding characteristics of IgGs binding to four different antigens. -- Fig. S6. Multabody v2 features. -- Fig. S7. PsV neutralization and inhibition of primary PBMC infection by Multabodies. -- Table S1. IC50 of individual and IgG mixtures, PGDM1400/N6x10E8v4 trispecific and HIV-1 Multabodies against a 14-PsV panel and 25-PsV panel (additional 11 HIV-1 strains highly resistant to PGDM1400). -- Table S2. Potency of parental and IgG mixtures and T-01 Multabody versions against a 118-PsV panel., Peer reviewed

Loliinae samples used in the repetitive DNA analysis. Genome skimming paired-end (PE) reads per sample and PE reads selected by Repeat Explorer 2 per sample in each of the comparative analyses of the four Loliinae groups: Loliinae, BL (broad-leaved Loliinae), FL (fine-leaved Loliinae), Schedonorus., 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

Repeat Explorer 2 comparative analysis. Repeat content data for top clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus., 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 dataset is an Excel file with five sheets that contain the following information: Sheet 1 ("1st experiment, 3 strains"): MLH1 foci count per spermatocyte per mice, strain and diet Sheet 2 ("2nd experiment, B6 males"): MLH1 foci count per spermatocyte per C57BL/6 mice treated with two diets (2nd experiment). Columns indicate the mouse ID and number of spermatocytes analyzed in parenthesis. Sheet 3 ("intercrossover distances"): Interfocus distances in control mice (maintenance diet) of 3 strains. Values are shown as percentage of synaptonemal complex length. Sheet 4 ("synaptonemal c. length, 1st"): Total autosomal length of synaptonemal complexes per strain, control groups (maintenance diets) Sheet 5 ("synaptonemal c. length, 2nd"): Total autosomal length of synaptonemal complexes per diet in C57BL/6 mice (2nd experiment), We performed two studies: in the initial one, adult males from the three strains were analyzed for the effect of two diets on recombination (undernourishment (reduction to 50% daily intake) and breeding diets (Teklad Global 18% Protein Rodent Diet)) provided during 24 days relative to a control group kept ad libitum with maintenance diet (Teklad Global 14% Protein Rodent Maintenance Diet). After the 24-day diet period, adult male mice were euthanized by cervical dislocation and weighed. After removing and weighing the testes, chromosome spreads for immunostaining as previously described (Anderson et al. 1999; de Boer et al. 2009; Milano et al. 2019). MLH1 immunostaining allows for identification of about 90% of mammalian crossover sites (Anderson et al. 1999; Cole et al. 2012). All slides were imaged on a Zeiss LSM 710 confocal microscope and analyzed using Zeiss Zen lite software. Only mid and mid-late pachytene stage spermatocytes were scored. For each spermatocyte, we counted the number of foci localizing to the SC of the 19 autosomes (Anderson et al. 1999); total SC length and interfocus distances were also measured in autosomes only., Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. We have explored for the first time the effect of dietary changes on crossover frequency per nucleus. Our study was performed in spermatocytes of 3 mouse inbred strains by analyzing the number and position of crossovers along the synaptonemal complexes, as well as the length of such synaptonemal complexes, by immunostaining with antibodies against MLH1 (which allows the identification of the crossover sites) and SYCP3 (a component of the synaptonemal complex). Our results show that male recombination rate is sensitive to dietary changes, and this sensitivity depends on the genetic background in mice. This is first to report a nutrition effect on genome-wide levels of recombination., Peer reviewed

Repeat Explorer 2 comparative analysis. Repeat content data for phylogenetically analyzed clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus., 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

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