Resultados de investigación

Additional file 20: Fig. S11. Schematic showing the position of the 2.5 kb APRE7-8 within the otd locus on the X chromosome of D. melanogaster. A 1.5 kb region shown to drive similar expression to the 2.5 kb region is indicated by a purple bar (37). Below is shown the ATAC-seq profile for this region and the positions of potential fixed mutations specific to D. mauritiana (arrows indicate SNPs and rectangles indicate short indels) with predicted binding sites for Otd, So and Cut in D. melanogaster indicated by arrows. Binding sites indicated with an asterisk contain mutations in D. mauritiana., Deutsche Forschungsgemeinschaft Biotechnology and Biological Sciences Research Council Ministerio de Ciencia, Innovación y Universidades European Research Council, Peer reviewed

Deutsche Forschungsgemeinschaft Biotechnology and Biological Sciences Research Council Ministerio de Ciencia, Innovación y Universidades European Research Council, Peer reviewed

Additional file 22: Table S10. Primers used to generate probes for in situ hybridization., Deutsche Forschungsgemeinschaft Biotechnology and Biological Sciences Research Council Ministerio de Ciencia, Innovación y Universidades European Research Council, Peer reviewed

Additional file 23: Table S11. Sequences used to generate reporter lines., Deutsche Forschungsgemeinschaft Biotechnology and Biological Sciences Research Council Ministerio de Ciencia, Innovación y Universidades European Research Council, Peer reviewed

Isotopic data are valuable to investigate species interactions and food web structure. This file compiles δ13C and δ15N values of various marine taxa; most of data correspond to mesopelagic fish, but mesopelagic cephalopods, decapods and zooplankton, and cetaceans are also represented. This dataset follows a previous data file presented in Silva et al. (2022b) (https://doi.pangaea.de/10.1594/PANGAEA.945917) and maintains the same layout. A total of 1045 records are included, of which 612 correspond to mesopelagic fish (55 species), 18 to non-mesopelagic fish (1 species), 168 to decapods (7 species), 68 to marine mammals (12 species), 5 to Cephalopoda (2 species) and 174 to zooplankton (14 taxa). Data are available for the subarctic and temperate Atlantic, the northeast Atlantic (off the Iberian Peninsula, Azores, and Bay of Biscay), and the Western Mediterranean. Samples come from years 2002 to 2021, and expand to all seasons. The table contains data on bulk stable isotope ratios of carbon (δ13C) and nitrogen (δ15N), and the total organic carbon to nitrogen ratio (C/N) measured in sample tissues or in the whole body of organisms are presented in this file. To eliminate the effect of lipids on δ13C values, lipids were extracted from samples before analysis (column "δ13C_LE (delipized)", or in other cases a mathematical correction was applied a posteriori (column "δ13C_Lipid Corrected"). For each data record, it is provided the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used., Horizon 2020 (H2020), grant/award no. 817806: Sustainable Management of Mesopelagic Resources (SUMMER). With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Minimum DEPTH, water: 0.5 m; Maximum DEPTH, water: 2000.0 m; 29SG20200929_Bongo_7B; Latitude: 38.074800; Longitude: -9.395600; Date/Time: 2020-10-17T20:40:00; Location: Sea off Lisbon, Atlantic Ocean; Campaign: 29SG20200929 (SUMMER); Basis: Sarmiento de Gamboa; Method/Device: Bongo net (BONGO) 29SG20200929_MOC01_1 (MOC01_1); Latitude Start: 38.470000; Longitude Start: 2.677000; Latitude End: 38.466700; Longitude End: 2.690300; Date/Time Start: 2020-09-30T14:20:00; Date/Time End: 2020-09-30T14:34:00; Mesh size: 2 mm; Location: Balear Sea; Campaign: 29SG20200929 (SUMMER); Basis: Sarmiento de Gamboa; Method/Device: MOCNESS opening/closing plankton net (MOC) 29SG20200929_MOC01_2 (MOC01_2); Latitude Start: 38.466700; Longitude Start: 2.690300; Latitude End: 38.466200; Longitude End: 2.701800; Date/Time Start: 2020-09-30T14:34:00; Date/Time End: 2020-09-30T14:47:00; Mesh size: 2 mm; Location: Balear Sea; Campaign: 29SG20200929 (SUMMER); Basis: Sarmiento de Gamboa; Method/Device: MOCNESS opening/closing plankton net (MOC), Peer reviewed

“Acari.csv“ This file contains counts of total acari (counts/500 mL soil), family level and functional groups. This data was used in Figure 1 and Table 2., “Bacteria_fungi_qPCR_Shannon.csv” This file contains quantitative PCR data for bacterial and eukaryotic marker genes (copies/g soil) and Shannon diversity indices calculated from microbiome sequencing data. It was used in Table 2., “Grain_characteristics.csv” This file contains wheat grain characteristics after harvest. Grain yield in kg/ha, Grain C N S in %, Grain elements in mg/kg, grain B vitamins in ug/100 g, reported technological properties in %, other technological properties not reported on in %, mm, unitless or 10-4 J. This data is presented in Table 5., “Nematodes.csv” This files contains counts of total nematodes (counts/100 g soil), family level, functional groups, and functional indices in units reported in tables. It was used in Figure 1, Table 2, and Table 3. Further details to nematode functional indices reported are as follows: Maturity indices after Bongers, (1990): MI and M25. Indicate maturity of the nematode community along ecological succession. Ranges 1-5. SMI= Modification and qualification of the nematode maturity index for plant feed nematodes, after Yeates (1994). Soil Food Web indices after Ferris et al., (2010, 2001), Range 0-100: PPI, CI= Channel Index: indicator of fungal-mediated organic matter decomposition. BI= Basal Index: indicator of basal, perturbed soil food webs. EI= Enrichment Index: indicator of active bacterial-mediated OM decomposition, soil fertility. SI= Structure Index: indicator of structured soil food webs, with predators and omnivores. BIOM= BIOM: total nematode biomass / 100 g dry soil. CF= Composite footprint; the whole nematode community. EF= Based on the amount of C mineralized by the nematode community inferred by their biomasses. SF= Structure footprint; nematodes in higher soil food web levels. HF= Herbivore footprint: herbivore nematodes. FF= Fungivore footprint; fungivore nematodes. BF= Bacterivore footprint: bacterivore nematodes. PF= Predator footprint: predatory nematodes. OF= Omnivore footprint: omnivore nematodes. TOT= Tot no. nematodes/100g dry soil. Herb= % herbivores in the community. Fung= % fungivores in the community. Bact= % bacterivores in the community. Pred= % predators in the community. Omn= % omnivores in the community. S= Taxa richness (based on genera/families)., “Plant_characteristics_flowering.csv” This file contains wheat plant characteristics at flowering stage with above- and belowground methods. Aboveground and belowground data are in units as reported in Table 4. Note percentages are recorded as fraction of 100., “Soil_chemistry.csv” This file contains soil chemical parameters. Soil moisture and C N is reported in %. Soil elements are reported in mg/kg except Mg_cacl2, K20_cal, and P2O5_cal which are stored as mg/100g. This is presented in Table 1, “Soil_functionality.csv” This files contains community level physiological profiles and potential enzymatic activities. Community level substrate use/respiratory profile (CLPP) indices with prefix MR. Acronyms are substrates as follows: Basal=water, KGA= keto-glutaric acid, OA=oxalic acid, Xyl=xylan, Gluc=Glucose, NAG=N-acetyl-glucoseamine, Ala=alanine, ABA=amino-butyric acid. Values are reported as µg CO2-C g-1 soil h-1. Substrate induced microbial biomass is inferred from glucose amended units and conversion of mass CO2-C from SIR into Volume CO2 with Ideal gas law and standard temperature (25°C) and standard pressure (1.013 bar). Microbial biomass is inferred with following formula: MBC=(mass C*40.04)+0.37) according to Anderson & Domsch (1978). Potential enzymatic activity is with prefix EEA. Acronyms are as follows: BG=beta-glucosidase, CB=cello-biohydrolase, XYL=xylanase, NAG=n-acetyl-glucoseaminidase, LAP= leucine amino peptidase, P_cyc = neutral and alkaline phosphatases (measured as PHOs, omitted as identical to P_cyc), C-cyc=sum of C acting enzymes, N_cyc= sum of N acting enzymes. Values are reported in nmol substrate g-1 soil h-1. This data is presented in Table 3., Peer reviewed

Genome assembly and gene prediction of Rhizopus stolonifer BLUCD01 version 1., Peer reviewed

This repository contains the code and datasets used in the study 'Mutualism Breakdown Underpins Evolutionary Rescue in an Obligate Cross-Feeding Bacterial Consortium'. The dataset includes both raw and processed data, along with the scripts required to reproduce the analyses presented in the manuscript., Peer reviewed

This study was conducted with a second generation of Erodium cicutarium plants grown in the greenhouse. Seeds were collected in 2015 from six adult broadly spaced plants at two E. cicutarium natural populations located in Cazorla mountains (Jaén province, SE Spain): Puerto del Tejo (PT, 1590 m asl) and Nava de las Correhuelas (CH, 1625 m asl) distant ca. 10 km in straight-line. The first generation (F1) plants (N = 50 and 41 for PT and CH, respectively) were grown in pots (universal substrate COMPO SANA®, mixed in 3:1 with perlite); pots were grouped in trays which combined individuals from the two populations and were periodically rotated within the greenhouse (16h light; 25-20 °C) until the end of reproduction (ca. 6 months). Half of the trays were watered twice per week and the other half were watered once every 10-11 days, being sure that some offspring of every plant experienced the two water regimes. Autonomously self-pollinated fruits were collected in paper bags, and stored at room temperature. In October 2016, seeds from the offspring of six mothers from each of the two water regimes and population were selected (N = 24 families: 2 populations * 2 water maternal regimes * 6 F1-mothers), with each F1-mother having a sib in the other water regime (i.e., the same six wild-plants per population provide seeds for all treatment levels). A demethylation treatment was applied to half of the seeds in which scarified seeds were submerged in 150 µl of either Control (water with DMSO 97:3, v:v) or a 0.5 mM solution of 5-azacytidine (Sigma A2385-100mg; 5azaC hereafter) during 48 h at 4 °C, a temperature in which the compound is relatively stable. Twenty days after sowing, 288 seedlings (144 control and 144 treated with 5azaC) of these second generation (F2) were transplanted into 1L pots. Other F2 extra seedlings (N = 40) were collected a few days later and processed to confirm the efficiency of the demethylation treatment at this stage and the normal appearance of individuals that reached this stage (see results in Alonso et al., 2017). The recurrent drought treatment started three weeks after transplant, when seedlings were around six weeks old. For each maternal line (line, hereafter), half the offspring was watered at field capacity twice per week and half the offspring was watered at field capacity once every 10-11 d until the end of the experiment. The full design was a 2 x 2 factorial with three replicates per line. Flowering started one week after transplant and reached the peak (75 % individuals with flowers) at week 10. The experiment finished when plants were 17 weeks old and plants started showing signs of senescence. Further details on traits measured and statistical methods can be obtained in Alonso, C., M. Medrano, C. M. Herrera. 2025. A dynamic epigenetic perspective on above and below-ground phenotypic responses to drought: insights from global DNA methylation in Erodium cicutarium. Plant Biology., This dataset includes one file containing data on the results of an experimental study that combined the experimental application of a demethylating agent (5-azacytidine) at seed germination stage with recurrent drought following a 2 x 2 factorial design in Erodium cicutarium (Geraniaceae). We measured global DNA methylation in adult leaves and roots, and above- and below-ground phenotypic traits related to plant development (first leaf length, time to first flower, changes in leaf and inflorescence numbers over time) and final (static) phenotype (reproductive output, above and below-ground biomass)., Peer reviewed

This file contains all reviewer reports in order by version, followed by all author rebuttals in order by version. Version 0: Reviewer comments: Reviewer #1 (Remarks to the Author) The manuscript entitled “An Exceedingly Low-Coordinate Platinum(0)-Germylene for E–H Bond Activation and Catalytic Hydrodehalogenation” by Jesús Campos describes the E‒H bond activation facilitated by Platinum(0)-Germylene cooperation, resulting in the formation of Pt(II)-germyl compounds. The Pt/Ge complex 1 reacts with alkynes to form 1,2platinogermacyclobutadiene compounds (compound 7), which also serve as efficient catalysts in hydrodehalogenation reactions. The structural symmetry of these compounds has been analyzed using NMR, X-ray single crystal data, and computational studies. Overall, the chemistry is well-executed and well-described, with some improvements suggested below. I am pleased to support its acceptance in this journal. General Comments: Compound 1 has successfully catalyzed the dehalogenation reaction. Can the stoichiometric reaction product of 1 with aliphatic or aromatic halides be obtained? This might help in understanding the reaction mechanism better. The authors have investigated the catalytic potential of compound 1 in the hydrodehalogenation of aliphatic and aromatic halides. What about the hydrodefluorination of organic fluorides? All yields of reactions are reported in spectroscopic form and were performed at room temperature. Can the authors attempt to separate and purify the products at low temperature to confirm the actual isolation yield of each reaction? Page 4, Line 9: “consistent with reactivity studies …” needs correction. Page 6, Figure 4: States 5 equivalents of methanol. Supplementary Information S7, Compound 4: States 2 equivalents and 1 equivalent of methanol. The authors need further confirmation and correction. Page 5, Line 10: “[ArDippGeCl]2 reacts with water, methanol, and ammonia to yield mixtures of products.” The structural information of these mixtures is not provided. Page 8, Line 12: The structural formula “κ1 interaction” of compound 3 is not consistent with “the π-interaction with the flanking aryl ring is now closer to a κ2-coordination”. Page 12, Figure 9: Change “RCCH” on the arrow to “2 RCCH”. Reviewer #2 (Remarks to the Author) The manuscript by Campos and colleagues describes an intriguing Pt germylene species (1) which was prepared by substitution of tBu-ethylene with a germylene source (a germylene dimer). Unfortunately, complex 1 is thermally unstable, and accordingly, was not isolated as an analytically pure material, nor was it characterized by X-ray crystallography. When generated in situ, complex 1 reacts with bonds in various small molecules (including the N-H of NH3). The authors refer to this as "cooperative activation", though addition of bonds across metal-main group multiple bonds is well known and usually not described as cooperative activation. Related work by Tilley (e.g. Organometallics 2009 5082) was not referenced. Complex 1 also inserts alkynes into the Pt=Ge bond. While these complexes and related reaction chemistry are interesting, they are not particularly novel. The highest impact of this work, in my opinion, is the catalytic dehydrohalogenation, particularly the fact that alkyl substrates were used. In addition, chlorides worked reasonably well. The manuscript would benefit from additional computational work to elucidate the mechanism of the catalytic cycle. If that were included, I would support publication of this manuscript in Nature Chemistry. One final comment: the authors refer to complex 1 as "exceedingly low coordinate". Given that no X-ray crystal structure was obtained, and the aryl groups on both the P and Gemight interact with the metal centre, this is perhaps somewhat of an over-reach. Why not simply call it "low coordinate"? Reviewer #3 (Remarks to the Author) This manuscript by Campos and coworkers deals with a Pt(0)-germylene complex. It is coordinately unsaturated at both Pt and Ge, which makes it proned to E-H bond activation. H2, H2O, MeOH and NH3 are shown to readily add across the formal Pt=Ge linkage. Catalytic hydrodehalogenation is also reported, with both alkyl and aryl substrates. This is a very important and original piece of work. Small molecule activation by transition metal / main group compounds has several precedents and is no longer a big surprise, but applying such systems to synthetically useful catalytic transformations is rare and remarkable. All the more so that the Pt(0)-germylene complex works with alkyl and aryl substrates with H2 as reductant. The manuscript is pleasant to read, the work is of high scientific and technic quality. All compounds have been fully characterized. I for sure recommend publication of this work in Nature Communications but there is one point that requires consideration and should be addressed before publication. It is the link between the stoechiometric studies of E-H bond activation and the catalytic hydrodehalogenation. I agree with the authors that « a thorough mechanistic picture lies out of the scope of the present contribution », but the relevance of the cooperative activation of H2 by the Pt(0)-germylene complex to the catalytic transformation should be substantiated. All the more so that the authors point some observations suggesting the involvement of radical pathways. It would also be nice to extend the stoechiometric studies to the RX substrates as some of them may compete with H2 upon reaction with the Pt(0)-germylene complex. Minor corrections : - Some phrasings are inappropriate and require polishing. For example on page 4 : « … suggesting that this atom partly retains its Z-type character ». - I also recommend careful proofreading. I noticed several typos. Version 1: Reviewer comments: Reviewer #1 (Remarks to the Author) The authors have systematically introduced the E‒H bond activation and catalytic hydrodehalogenation applications of lowcoordinate platinum(0)-germylene, elucidating the catalytic reaction mechanism through detailed experimental and theoretical calculations. The authors have also addressed my questions regarding this work, and the manuscript has been thoroughly revised and is now suitable for acceptance. Reviewer #2 (Remarks to the Author) After carefully scrutinizing the revised version of the manuscript by Campos and colleagues, as well as the responses to all reviewer comments, I fully endorse its publication in Nature Communications. Every single comment was addressed in depth and a great deal of additional work was performed. The result is substantial improvement to an already excellent contribution. Reviewer #3 (Remarks to the Author) The authors have carefully revised their manuscript. They have taken into account and convincingly addressed all the comments raised by the reviewers. In my opinion, the paper can be published in Nature Communications as is., Pairing transition metals and heavier tetrylenes (Si, Ge, Sn, Pb) holds great potential for cooperative bond activation and catalysis. In this work, we investigate the reactivity of a low-coordinate Pt(0)/Ge(II) system that emerges from the reaction between the monoligated platinum(0) precursor [(PMe2ArDipp2)Pt(olefin)] with germylene dimer [ArDipp2GeCl]2 (where ArDipp2 = C6H3-2,6-(C6H3-2,6-iPr2)2). The resulting complex reveals ability for cooperative bond activation. Stoichiometric reactions with dihydrogen, water, methanol, ammonia and alkynes unveil the formation of Pt(II)-germyl compounds, characterized by distinct isomeric forms, whose flexibility derives from the particularly low-coordination. We explore its catalytic potential in the hydrodehalogenation of aliphatic, aromatic and main-group halides under dihydrogen atmosphere using both thermal and photochemical conditions, demonstrating promising conversions even for more challenging alkyl chlorides. Pairing transition metals and heavier tetrylenes holds potential for cooperative bond activation. Here, the authors investigate the reactivity of a low-coordinate Pt(0)/Ge(II) system that emerges from the reaction between a monoligated platinum(0) precursor with a germylene dimer and explore its application as a hydrodehalogenation catalyst., This work has been supported by the European Research Council (ERC Starting Grant, CoopCat, 756575; JC), the Spanish Ministry of Science and Innovation (PID2022-139782NB-I00; JC, and TED2021-132225B-I00; JC) and Junta de Andalucia (P18-FR-4688; JC). We also acknowledge the European Commission for a MSCA fellowship (101023461; SB), and the use of computational resources of the CSIRC of the Universidad de Granada -cluster Albaicín-. We thank Lamin Keita for his assistance on ligand and precursor synthesis., Peer reviewed