Resultados totales (Incluyendo duplicados): 33862
Encontrada(s) 3387 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331417
Dataset. 2022

TABLE_5_A NOVEL GENE SIGNATURE UNVEILS THREE DISTINCT IMMUNE-METABOLIC REWIRING PATTERNS CONSERVED ACROSS DIVERSE TUMOR TYPES AND ASSOCIATED WITH OUTCOMES.DOCX [DATASET]

  • Pedrosa, Leire
  • Foguet, Carles
  • Oliveres, Helena
  • Archilla, Iván
  • García de Herreros, Marta
  • Rodríguez, Adela
  • Postigo, Antonio
  • Benítez-Ribas, Daniel
  • Camps, Jordi
  • Cuatrecasas, Miriam
  • Castells, Antoni
  • Prat, Aleix
  • Thomson, Timothy M.
  • Maurel, Joan
  • Cascante, Marta
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331417
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331417
HANDLE: http://hdl.handle.net/10261/331417
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331417
PMID: http://hdl.handle.net/10261/331417
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331417
Ver en: http://hdl.handle.net/10261/331417
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331417

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331419
Dataset. 2022

SUPPLEMENTARY MATERIAL FOR AVOIDANCE OF NEONICOTINOID-TREATED SEEDS AND COTYLEDONS BY CAPTIVE EARED DOVES (ZENAIDA AURICULATA, COLUMBIDAE)

  • Addy-Orduna, Laura M.
  • Cazenave, Jimena
  • Mateo, Rafael
Fig. S1. Conceptual model of avoidance. A primary repellent evokes reflexive withdrawal immediately after exposure. A secondary repellent is avoided because an animal associates a conditional stimulus (sound, sight, taste) to an aversive experience (e.g., illness, pain) with a sensory stimulus. A generalized conditional aversion may occur against the food that previously contained the chemical and it is avoided by only the type of food as the cue to refusing it. Fig. S2. Diagram of test of avoidance to treated sorghum seeds. Fig. S3. Diagram of experiment of avoidance to soybean seeds treated with imidacloprid. Fig. S4. Diagram of experiment of avoidance to soybean cotyledons treated with neonicotinoids. Fig. S5. Frequency of signs of intoxication observed over the days in each treatment during the Exposure 1 (A) and Exposure 2 (B) periods of the sorghum experiment. Signs of intoxication were measured as present or absent at each moment of observation, consisting of from lethargy to motionless. Letters indicate significant differences among treatments. IMI: red bars, CLO: green bars, THI: blue bars. Fig. S6. Body weights of survivors and dead in the sorghum experiment. The deaths only occurred in the sorghum experiment, during the Exposure 1 period, in birds treated with imidacloprid (3 dead) and clothianidin (1 dead). In the dead, the BWs were measured at the time of death. In survivors, BWs were measured at the end of the Exposure 1 period. Table S1. Records of maximum and minimum temperature and humidity in each period, and average daily thermal amplitude. Table S2. Doves that consumed soybeans (12 of the 40). Consumption was measured from the fourth day of the "Pre-Exposure 1" period. The number of seeds consumed was calculated based on the average daily weight of soybeans used to measure the humidity factor. Table S3. Average mass in grams of seeds and cotyledons. "Ad Sur" sorghum is the AD75STA commercial hybrid sorghum of "adSur, Agrosemillas del Sur SA", used in COM, IMI and THI treatments of the sorghum test. “DK” sorghum is the “Dekalb” commercial hybrid sorghum seeds of Syngenta®, used in CLO treatment of the sorghum test. Table S4. Average consumption in grams (mean ± SE) of test food and the total consumption (grams of test food + grams of maintenance food) during periods of exposure to neonicotinoids. In the sorghum seeds, CON is the untreated sorghum control and COM is the commercial sorghum control. Table S5. Video records of the behavior of some doves during the first 15 minutes of exposure to food in the different treatments and periods. “1rt peck” indicates the time in seconds when the bird first pecked at the food inside the feeder after it was offered; “n peck food” is the number of times the bird pecked at the feeder food during the first 15 minutes of its exposure to the food; “n grit peck” is the number of times the bird pecked at the grit; “n drink” is the number of times the bird drank water from the drinking fountain; “n grooming” is the number of times the bird groomed itself; “n shaking” is the number of times the bird shook; “on perch” is the number of times the bird climbed on the perch. In the sorghum experiment, CON is the untreated sorghum control and COM is the commercial sorghum control. Table S6. Body condition index (SMI) and the p-value of the paired Wilcoxon test used to compare the initial and final body conditions of each treatment in the three experiments. In the sorghum experiment, CON is the untreated sorghum control and COM is the commercial sorghum control., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/331419
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331419
HANDLE: http://hdl.handle.net/10261/331419
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331419
PMID: http://hdl.handle.net/10261/331419
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331419
Ver en: http://hdl.handle.net/10261/331419
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331419

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331421
Dataset. 2022

SUPPLEMENTARY TABLES OF THE ARTICLE ISOTOPIC NICHE PROVIDES AN INSIGHT INTO THE ECOLOGY OF A SYMBIONT DURING ITS GEOGRAPHIC EXPANSION [DATASET]

  • González-Ortegón, Enrique
  • Pérez-Miguel, Marta
  • Navas, Jose I.
  • Drake, Pilar
  • Cuesta, José A.
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331421
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331421
HANDLE: http://hdl.handle.net/10261/331421
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331421
PMID: http://hdl.handle.net/10261/331421
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331421
Ver en: http://hdl.handle.net/10261/331421
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331421

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331427
Dataset. 2022

SUPPLEMENTARY INFORMATION FOR ENGINEERING PAN-HIV-1 NEUTRALIZATION POTENCY THROUGH MULTISPECIFIC ANTIBODY AVIDITY

  • Rujas, Edurne
  • Cui, Hong
  • Burnie, Jonathan
  • Burn Aschner, Clare
  • Zhao, Tiantian
  • Insausti, Sara
  • Muthuraman, Krithika
  • Semesi, Anthony
  • Ophel, Jasper
  • Seaman, Michael S.
  • Guzzo, Christina
  • Treanor, Bebhinn
  • Julien, Jean-Philippe
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331427
HANDLE: http://hdl.handle.net/10261/331427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331427
PMID: http://hdl.handle.net/10261/331427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331427
Ver en: http://hdl.handle.net/10261/331427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331427

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331428
Dataset. 2022

DATA_SHEET_1_EVOLUTIONARY DYNAMICS OF THE REPEATOME EXPLAINS CONTRASTING DIFFERENCES IN GENOME SIZES AND HYBRID AND POLYPLOID ORIGINS OF GRASS LOLIINAE LINEAGES.PDF

  • Moreno Aguilar, María Fernanda
  • Inda, Luis A.
  • Sánchez-Rodríguez, Aminael
  • Arnelas, Itziar
  • Catalán, Pilar
36 pages. -- Supplementary Figure 1 | (A) Combined (plastome + 35S rDNA) Loliinae coalescent species tree computed through Singular Value Decomposition quartets (SVDq) analysis showing bootstrap support values on branches. (B–D) Maximum Likelihood phylogenomic trees of 47 Loliinae samples based on (B) Combined (plastome + 35S rDNA) data, (C) plastome data, (D) nuclear 35S rDNA data, (E) Histograms of repeat contents per holoploid genome (1C) retrieved from the individual Repeat Explorer 2 analyses of the studied Loliinae samples mapped onto the Maximum Likelihood combined phylogenomic tree (plastome + nuclear 35S rDNA cistron) of Loliinae. -- Supplementary Figure 2 | Correlation plots of repeat content and genome size variation (1Cx) for the 23 Loliinae taxa with known genome sizes. -- Supplementary Figure 3 | Evolutionary networks based on standardized repeat data sets obtained from the comparative RE2 analysis of the four Loliinae evolutionary groups: (A) Loliinae, (B) broad-leaved (BL) Loliinae, (C) fine-leaved (FL) Loliinae, (D) Schedonorus. -- Supplementary Figure 4 | Maximum Likelihood Loliinae tree cladograms (combined plastome + nuclear 35S rDNA cistron) showing the relationships among the studied samples in each of the four evolutionary groups of Loliinae and phyloheatmaps of normalized values for different sets of repeat clusters retrieved by RE2 from the comparative analysis of each group: (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). -- Supplementary Figure 5 | Maximum Likelihood nuclear 5S rDNA cistron tree showing the relationships among the 47 studied Loliinae samples., 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

Proyecto: //
DOI: http://hdl.handle.net/10261/331428
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331428
HANDLE: http://hdl.handle.net/10261/331428
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331428
PMID: http://hdl.handle.net/10261/331428
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331428
Ver en: http://hdl.handle.net/10261/331428
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331428

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331429
Dataset. 2022

TABLE_1_EVOLUTIONARY DYNAMICS OF THE REPEATOME EXPLAINS CONTRASTING DIFFERENCES IN GENOME SIZES AND HYBRID AND POLYPLOID ORIGINS OF GRASS LOLIINAE LINEAGES.DOCX

  • Moreno Aguilar, María Fernanda
  • Inda, Luis A.
  • Sánchez-Rodríguez, Aminael
  • Arnelas, Itziar
  • Catalán, Pilar
Taxa included in the repeatome analysis of Loliinae. Taxonomic rank, taxon authorship, detailed localities and vouchers, and source of cytogenetic and genomic data. Group: BL, broad-leaved Loliinae; FL, fine-leaved Loliinae; Sch, Schedonorus. Chromosome number (2n), ploidy, genome size (2C, pg), monoploid genome size (1Cx, pg; 1Cx, Mbp) and GenBank accession codes for plastome and nuclear ribosomal 35S and 5S genes are given for each sample. Values in bold correspond to new data generated in this study. Outgroups used in the phylogenomic analyses: Oryza sativa, Brachypodium distachyon., 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

Proyecto: //
DOI: http://hdl.handle.net/10261/331429
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331429
HANDLE: http://hdl.handle.net/10261/331429
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331429
PMID: http://hdl.handle.net/10261/331429
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331429
Ver en: http://hdl.handle.net/10261/331429
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331429

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331430
Dataset. 2022

TABLE_2_EVOLUTIONARY DYNAMICS OF THE REPEATOME EXPLAINS CONTRASTING DIFFERENCES IN GENOME SIZES AND HYBRID AND POLYPLOID ORIGINS OF GRASS LOLIINAE LINEAGES.DOCX

  • Moreno Aguilar, María Fernanda
  • Inda, Luis A.
  • Sánchez-Rodríguez, Aminael
  • Arnelas, Itziar
  • Catalán, Pilar
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331430, https://doi.org/10.20350/digitalCSIC/15443
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331430
HANDLE: http://hdl.handle.net/10261/331430, https://doi.org/10.20350/digitalCSIC/15443
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331430
PMID: http://hdl.handle.net/10261/331430, https://doi.org/10.20350/digitalCSIC/15443
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331430
Ver en: http://hdl.handle.net/10261/331430, https://doi.org/10.20350/digitalCSIC/15443
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331430

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331431
Dataset. 2022

TABLE_3_EVOLUTIONARY DYNAMICS OF THE REPEATOME EXPLAINS CONTRASTING DIFFERENCES IN GENOME SIZES AND HYBRID AND POLYPLOID ORIGINS OF GRASS LOLIINAE LINEAGES.XLSX

  • Moreno Aguilar, María Fernanda
  • Inda, Luis A.
  • Sánchez-Rodríguez, Aminael
  • Arnelas, Itziar
  • Catalán, Pilar
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331431
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331431
HANDLE: http://hdl.handle.net/10261/331431
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331431
PMID: http://hdl.handle.net/10261/331431
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331431
Ver en: http://hdl.handle.net/10261/331431
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331431

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331433
Dataset. 2021

RECOMBINATION STUDY BY MLH1 IMMUNOSTAINING OF MOUSE SPERMATOCYTES AFTER DIETARY TREATMENTS

  • Casa-Esperon, Elena de la
  • Belmonte-Tebar, Angela
  • San Martin Perez, Estefania
  • Nam Cha, Syonghyun
  • Soler, Ana J.
  • Singh, Nadia D.
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331433
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331433
HANDLE: http://hdl.handle.net/10261/331433
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331433
PMID: http://hdl.handle.net/10261/331433
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331433
Ver en: http://hdl.handle.net/10261/331433
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331433

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331434
Dataset. 2022

TABLE_4_EVOLUTIONARY DYNAMICS OF THE REPEATOME EXPLAINS CONTRASTING DIFFERENCES IN GENOME SIZES AND HYBRID AND POLYPLOID ORIGINS OF GRASS LOLIINAE LINEAGES.XLSX

  • Moreno Aguilar, María Fernanda
  • Inda, Luis A.
  • Sánchez-Rodríguez, Aminael
  • Arnelas, Itziar
  • Catalán, Pilar
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

Proyecto: //
DOI: http://hdl.handle.net/10261/331434
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331434
HANDLE: http://hdl.handle.net/10261/331434
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331434
PMID: http://hdl.handle.net/10261/331434
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331434
Ver en: http://hdl.handle.net/10261/331434
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331434

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