BUSCADOR RECOLECTA

(A) CBK1-GFP cdc15-2 (YMF3566) and CBK1-GFP TOR1-1 cdc15-2 (YMF3565) cells were grown in YPD and arrested in late anaphase by shifting the temperature to 37 °C before the addition of rapamycin for 20 min to both strains. In addition, DMSO was added to one half of CBK1-GFP cdc15-2. Untagged cdc15-2 (YMF3580) and TOR1-1 cdc15-2 cells (YMF3578) were used as controls. Cell extracts were prepared before the immunoprecipitation of Cbk1-GFP on ChromoTek GFP-Trap Magnetic beads. Isolated material was subjected to analysis by mass spectrometry. Numbers represent spectral average of key Cbk1 functional-related interactors in 3 independent replicates of the experiment. The average is calculated as the sum of all spectral counts for the 3 replicates divided by 3. We found Cbk1 interactions previously described: Mob2 [48] or components of the RAM pathway such as Tao3 [97], Sog2 [98], and Kic1 [99]. Besides, Cbk1 negative regulators Lre1 and Fir1 were also identified [5,43]. Besides, MS found Myo1, a component of the actomyosin ring [43]. Our results showed that Cbk1 interacts with the transcription factor Ace2 [47,48]. Moreover, Cbk1 was bound to Ssd1, an RNA-binding protein that represses the translation of cell wall remodelling proteins until Ssd1 is phosphorylated by Cbk1 [48,100]. Interestingly, TORC1 and Ssd1 have been described to collaborate to maintain cellular integrity [73]. We found interactions with paralogs serine/threonine kinases Kin1 and Kin2 [74,75]. Finally, we detected protein Yol036w of unknown function interacting with Cbk1 [40,74]. Details of other known Cbk1 interactors are shown in S2 Table. (B) CBK1-5FLAG ACE2-HA cdc15-2 (YMF3585) and control cells (YMF3587) (i), CBK1-5FLAG MOB2-9MYC cdc15-2 (YMF3838) and control cells (YMF3835) (ii), or CBK1-TAP SOG2-6HA cdc15-2 (YMF4235) and control cells (YMF4236) cells (iii) were grown in YPD and arrested in late anaphase by shifting to 37 °C before the addition of rapamycin for 20 min when indicated. Subsequently, protein extracts were prepared and immunoprecipitations of Cbk1 on FLAG-beads or IgG beads (as denoted) were performed before the detection of the indicated proteins by immunoblotting. Raw data for blots can be found in Supporting information (S7 Raw Images). (C) Components of TORC1 were found in the same mass spectrometry analysis as in A. Numbers represent spectral average of 3 independent replicates of the experiment., pbio.3002263.s008.pdf, Peer reviewed

1 file, Supplementary information for the article https://doi.org/10.1038/s41598-020-57501-0, Table S1. Primer sequences used for qPCR.-- Supplementary Figure S1. Antiviral activity of the CRP1-7-depleted supernatants.-- Supplementary Figure S2. Assessment of the ability of CRP-mix to induce the transcription of ifnphi1 and ifnphi2 in vitro.-- Supplementary Figure S3. Assessment of the ability of IL-6 to induce the expression of crp1-7 transcripts in vivo.-- Supplementary Figure S4. Transcriptional modulation of autophagy by SVCV in the ZF4 cells.-- Supplementary Figure S5. Effect of the addition of exogenous cholesterol on intracellular autophagosome levels and SVCV infection in vitro, Peer reviewed

Number and frequency of visits to Pyrus bourgaeana trees in southern Spain. The number of visits has been added to this file for first time., PID2022-142067NB-I00 CGL2017- 84633- P FPU17/04375, Peer reviewed

Lateral views of adult eyes (a-c) and L3 eye discs, stained with Dcp-1 (and counterstained with rhodamine phalloidin, “actin”) (a’-c’) of the indicated genotypes. (d) Distribution of apoptosis intensity in L3 discs of the indicated genotypes. Blocking apoptosis driving the UAS-RHG-RNAi reduces the apoptosis caused by tkv attenuation (optix>tkvRI + RHGRI). The statistical analysis corresponding to these data can be found in S2 Table. (*): p < 0.05; (**): p < 0.01; (***): p < 0.001. The data underlying the graphs shown in the figure can be found in “Fig 2_data” in the Supporting information file S1 Raw Data., Peer reviewed

First block shows each genotype’s effect on the rE median, their p.values, and the predicted median for each of them. The second and third blocks show the standard deviation of each group for rE and sFAi, respectively, and the result of the comparison of variances of each group against the optix>+ reference group., Peer reviewed

[Description of methods used for collection/generation of data] Download from publicly available sources, with analysis, statistical inference and assembly with Python., [Methods for processing the data] Python executed in Jupyter notebooks., We use a multilayer network approach to build digital twins of 5 Spanish cities (Barcelona, Valencia, Sevilla, Zaragoza and Murcia), describing them at the level of individuals, who have specific ages, sexes and home districts. We inferred interactions among individuals using publicly available data and statistics linked to home, school, university, work, community and nursing homes contexts (layers). This dataset includes the source data and codes needed for building the digital twins, together with individual metadata and the link lists associated with each city and each layer., JR, AA, and YM acknowledge support from the Government of Aragon (FONDO–COVID19-UZ-164255). JR is supported by Govern de les Illes Balears through the Vicenç Mut program and the María de Maeztu Excellence Unit 2023-2027 Ref. CEX2021-001164-M, funded by MCIN/AEI/ 10.13039/501100011033. AA acknowledges support through the grant RYC2021-033226-I funded by MCIN/ AEI/ 10.13039/501100011033 and the European Union NextGenerationEU/PRTR. YM was partially supported by the Government of Aragon, Spain, and ERDF "A way of making Europe" through grant E36-20R (FENOL), and by Ministerio de Ciencia e Innovación, Agencia Española de Investigación (MCIN/AEI/ 10.13039/501100011033) Grant No. PID2020-115800GB-I00. The authors acknowledge the use of the computational resources of COSNET Lab at Institute BIFI, funded by Banco Santander through grant Santander-UZ 2020/0274, and by the Government of Aragon (FONDO–COVID19-UZ-164255). JR and AA acknowledge funding from la Caixa Foundation under the project code SR20-00386 (COVID-SHINE)., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2021-001164-M)., citydigitwin.zip, Peer reviewed

Results of the beta regression, assessing the effect of NewAlters on the Abstract Similarity Score., Peer reviewed

Additional file 10. BED file with stable and differential HiChIP loops in neural retina and RPE/choroid, with annotation of interacting cis-regulatory elements (CREs, from [4])., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Same conditions as in S1 Table. We found Cbk1 described interactions in cdc15-2 cells in the absence (A “cdc15-2 vs. control”), the presence of rapamycin (B “cdc15-2 + rapa vs. ctrl”), and TOR1-1 cdc15-2 cells after the addition of rapamycin (C “TOR1-1 cdc15-2 + rapa vs. ctrl”). In all cases, cells were arrested in late anaphase after having been grown at 37 °C. Three biological replicates of each described cells and conditions were performed and compared with 3 biological replicates of untagged control cells (ctrlCounts). Cbk1 interactions can be found in: https://thebiogrid.org/35668/summary/saccharomyces-cerevisiae/cbk1.html., Peer reviewed

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