Resultados totales (Incluyendo duplicados): 33743
Encontrada(s) 3375 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343461
Dataset. 2023

S1 FIG. EXPERIMENTAL SET-UP AND DIFFERENTIALLY EXPRESSED GENES (DEGS)

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
A) RNA sampling conditions from environmental (soil and mineral water) and previously obtained samples (rich B medium reference and three in planta conditions). B) Transcriptomic data analysis pipeline. First, raw RNA-seq data quality was evaluated with FastQC (v.0.11.5), trimmed with trimGalore (v.0.6.1) and potential rRNA contaminants were filtered out with the SortMeRNA software (v.4.2.0). Reads were mapped with Bowtie2 (v. 2.4.4) and alignments quantified with FADU v. 1.8. The R. solanacearum UY031 genome GCF_001299555.1_ASM129955v1 was used. DEG analyses were performed with Deseq2 (v. 1.34.0). Genes with |log2(fold-change)|>1.5 and adjusted p-value <0.01 were considered as differentially expressed (DEG) when compared to the reference medium. The UpsetR package (v. 1.4.0) (90) was used to detect unique DEG and intersections among the in the different conditions. Deseq2 transformed counts normalized for sample size were used for principal component analysis. C) DEGs in the different conditions. Bars show the total number of up- (yellow) and downregulated (blue) genes for each condition compared to the reference Rich B medium. The line graph and the right Y axis indicate the percentage of DEGs. Drawings created with BioRender., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343461
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343461
HANDLE: http://hdl.handle.net/10261/343461
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343461
PMID: http://hdl.handle.net/10261/343461
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343461
Ver en: http://hdl.handle.net/10261/343461
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343461

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343475
Dataset. 2023

S2 FIG. GO AND KEGG ENRICHMENT ANALYSES OF THE ENVIRONMENTAL CONDITIONS

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
Dot plots of the KEGG (left) and GO (right) enrichment analyses of differentially expressed genes (DEGs) from soil (brown) and water (blue) conditions. Dot sizes represent the number of genes associated with each term and dot colour indicates the p. adjusted value. The gene ratio represented in the X axis is the proportion of associated genes to a term from the total gene set. The DEGs were extracted with DEseq2 using the thresholds: p-adj.value > 0.01 and log 2 FC ± 1.5 and ClusterProfiler was used to calculate the enrichment., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343475
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343475
HANDLE: http://hdl.handle.net/10261/343475
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343475
PMID: http://hdl.handle.net/10261/343475
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343475
Ver en: http://hdl.handle.net/10261/343475
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343475

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343477
Dataset. 2023

S3 FIG. TIME-COURSE EXPRESSION OF THE PHRPB::LUX REPORTER IN STRAINS DISRUPTED FOR THE DIFFERENT T3SS REGULATORY GENES AFTER RESUSPENSION IN WATER

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
R. solanacearum cultures grown overnight in rich B medium were washed and diluted to OD600 = 0.1 in water and luminescence and OD600 values were measured over a 24h period. Relative luminescence units (RLU) were normalised by bacterial concentration measured as OD600. RLU values were divided by 1000 to facilitate visualisation., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343477
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343477
HANDLE: http://hdl.handle.net/10261/343477
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343477
PMID: http://hdl.handle.net/10261/343477
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343477
Ver en: http://hdl.handle.net/10261/343477
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343477

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343488
Dataset. 2023

S4 FIG. INDUCTION OF THE TYPE 3 SECRETION SYSTEM (T3SS) BY BASIC PH IN ALL NATURAL WATER SOURCES TESTED

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
Time-course expression of prhG, hrpB and hrpY reporter strains at native basic (A to F) or neutral pH (G) and after pH neutralisation with HCl or alkalinisation with KOH. For each time point, luminescence was measured (RLU) and normalised by OD600. All values were divided by 1000 to facilitate visualisation. Letters indicate the water sources detailed in the methods section., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343488
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343488
HANDLE: http://hdl.handle.net/10261/343488
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343488
PMID: http://hdl.handle.net/10261/343488
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343488
Ver en: http://hdl.handle.net/10261/343488
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343488

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343492
Dataset. 2023

S5 FIG. INDUCTION OF NITROGEN METABOLISM GENES IN SOIL

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
A) Representation of the main components of the nitrogen metabolism and their expression in different conditions (log2 fold change with respect to rich B medium). Genes depicted in A correspond to genes highlighted in bold in B. B) Heatmap representation of the log2 fold change in expression with respect to growth in rich B medium for all the genes classified in the nitrogen metabolism group. The colour palette ranges from blue (downregulated) to yellow (upregulated genes) as indicated in the key. Locus names are presented without the preceding letters RSUY_., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343492
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343492
HANDLE: http://hdl.handle.net/10261/343492
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343492
PMID: http://hdl.handle.net/10261/343492
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343492
Ver en: http://hdl.handle.net/10261/343492
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343492

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343494
Dataset. 2023

NEURAL-NETWORK FORCE FIELD BACKED NESTED SAMPLING: STUDY OF THE SILICON P-T PHASE DIAGRAM. SUPPLEMENTARY MATERIAL

  • Unglert, Nico
  • Carrete, Jesús
  • Pártay, Livia B.
  • Madsen, Georg K.H.
Analysis of phases visited during the nested sampling algorithm., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343494
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343494
HANDLE: http://hdl.handle.net/10261/343494
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343494
PMID: http://hdl.handle.net/10261/343494
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343494
Ver en: http://hdl.handle.net/10261/343494
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343494

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343496
Dataset. 2023

S6 FIG. EXPRESSION OF ALL STRESS RESPONSE AND THE TYPE 3 SECRETION SYSTEM (T3SS) AND TYPE 3 EFFECTOR GENE GROUPS

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
Heatmap representation of gene log2 fold change with respect to the rich B medium in the different conditions for A) All stress response genes and B) T3SS and T3E gene categories according to the curated classification (see M&Ms). The colour palette ranges from blue (downregulated) to yellow (upregulated genes) as indicated in the key. Locus names are presented without the preceding letters RSUY_., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343496
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343496
HANDLE: http://hdl.handle.net/10261/343496
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343496
PMID: http://hdl.handle.net/10261/343496
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343496
Ver en: http://hdl.handle.net/10261/343496
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343496

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343500
Dataset. 2023

S7 FIG. EXPRESSION OF KEY GENES ASSOCIATED WITH OXIDATIVE STRESS IN SOIL AND WATER AT 3 DPI

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
Real time q-PCR was performed to validate gene expression in soil and water at 3 dpi. The genes selected were ahpC (RSUY_35830), katE (RSUY_45660), katG (RSUY_09930) and oxyR (RSUY_07740). Relative expression of target genes was calculated with the DeltaCt method using the geometric mean of the housekeeping gene serC (RSUY_11010) as reference. Error bars represent standard error across three technical replicates., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343500
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343500
HANDLE: http://hdl.handle.net/10261/343500
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343500
PMID: http://hdl.handle.net/10261/343500
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343500
Ver en: http://hdl.handle.net/10261/343500
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343500

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343503
Dataset. 2024

SUPPLEMENTAL MATERIAL: MACHINE-LEARNING-BOOSTED AB-INITIO STUDY OF THE THERMAL CONDUCTIVITY OF JANUS PTSTE VAN DER WAALS HETEROSTRUCTURES

  • Pan, Lijun
  • Carrete, Jesús
  • Wang, Zhao
  • Madsen, Georg K.H.
Parity plots of the neural-network force field, phonon spectrum and anharmonic scattering rates of the AB-stacked PtS2 bilayer, comparison of ab-initio vs. machine-learning phonon dispersions of monolayers and bilayers, and illustration of the effect of classical (equipartition) occupations., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343503
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343503
HANDLE: http://hdl.handle.net/10261/343503
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343503
PMID: http://hdl.handle.net/10261/343503
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343503
Ver en: http://hdl.handle.net/10261/343503
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343503

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343508
Dataset. 2023

S8 FIG. VIABILITY OF R. SOLANACEARUM CELLS IN SOIL MICROCOSMS

  • Pedro-Jové, Roger de
  • Corral, Jordi
  • Rocafort, Mercedes
  • Puigvert, Marina
  • Azam, Fàtima Latif
  • Vandecaveye, Agustina
  • Macho, Alberto P.
  • Balsalobre, Carlos
  • Coll, Núria S.
  • Orellano, Elena G.
  • Valls, Marc
A) Representative confocal laser scanning microscope images of bacterial cells extracted from soil microcosms at 28 dpi. Cells were stained using the BacLight LIVE/DEAD bacterial viability kit. Green cells represent viable cells and red represents dead cells. Scale bar represents 50 μm. B) Quantification of dead cells at different time points of soil microcosms based in BacLight LIVE/DEAD staining. Cells were quantified using Fiji ImageJ. Detailed methods:0.5 g from soil microcosms experiments was resuspended with 1 mL MilliQ water, samples were vortexed and soil particles allowed to sediment. Supernatants were recovered, centrifuged at 1000 rpm for 5 min to eliminate soil and supernatant was transferred to a fresh tube and cells were pelleted by centrifugation at 10000 rpm, 5 min and finally, cells were resuspended in 300 μL 0.85% NaCl. Then, 50 μL of cells were stained with 0.2 μL of BacLight LIVE/DEAD bacterial viability kit (ThermoFisher), incubated for 5 min in the dark and visualized promptly with a confocal microscope. Green SYTO9 fluorescence was measured with excitation at 488 nm and emission at 500–520 nm and red PI fluorescence was measured by excitation at 561 nm and emission at 610–630 nm. The alive control was prepared by washing an overnight culture with 0.85% NaCl and the dead control was prepared by killing cells from the overnight culture with 70% isopropanol for 1 h, followed by centrifugation of cells and resuspension in 0.85% NaCl. The number of alive and dead cells was quantified using ImageJ by setting a “threshold method = Moments” and particles size = 0.5-Infinity., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/343508
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343508
HANDLE: http://hdl.handle.net/10261/343508
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343508
PMID: http://hdl.handle.net/10261/343508
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343508
Ver en: http://hdl.handle.net/10261/343508
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/343508

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