BUSCADOR RECOLECTA

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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Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes., Peer reviewed

[Introduction]: In monoclonal B cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), the expansion of malignant B cells disrupts the normal homeostasis and interactions between B cells and T cells, leading to immune dysregulation. CD20+ T cells are a subpopulation of T cells that appear to be involved in autoimmune diseases and cancer., [Methods]: Here, we quantified and phenotypically characterized CD20+ T cells from MBL subjects and CLL patients using flow cytometry and correlated our findings with the B-cell receptor mutational status and other features of the disease., [Results and discussion]: CD20+ T cells were more represented within the CD8+ T cell compartment and they showed a predominant memory Tc1 phenotype. CD20+ T cells were less represented in MBL and CLL patients vs healthy controls, particularly among those with unmutated IGVH gene. The expansion of malignant B cells was accompanied by phenotypic and functional changes in CD20+ T cells, including an increase in follicular helper CD4+ CD20+ T cells and CD20+ Tc1 cells, in addition to the expansion of the TCR Vβ 5.1 in CD4+ CD20+ T cells in CLL., Peer reviewed

Detailed composition for each substrate-binding pocket in AmiA:peptide 5 complex., Peer reviewed