As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on not only antitubercular potency but also on physicochemical characteristics. The 50 most attractive compounds were then progressed for evaluation in three different predictive computational...

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...

The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and...

Additional file 3: Supplementary Table 1. Characteristics of the study participants with information for cognition outcomes. Mean and SD are shown for continuous variables. Supplementary Table 2. Characteristics of the study participants with information for neuroimaging outcomes. Mean and SD are shown for continuous variables. Supplementary Table 3. Characteristics of the study participants with information for CSF biomarkers. Mean and SD are shown for continuous variables.

Additional file 5: Supplementary Figure 1. Leave-one-out permutation analysis plot for AD signature among individuals at high genetic predisposition to AD obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest of the instrumental variables. Supplementary Figure 2. Leave-one-out permutation analysis plot for Aging signature among individuals at high genetic predisposition to AD, obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest...

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning...

Additional file 2: Figure S1. BraLan3 genome assembly and annotation quality comparison. Drer, Ggal, Mmus, Hsap, Bflo and Bbel correspond to the latest available genome assemblies for zebrafish, chicken, mouse, human, Florida amphioxus (B. floridae) and an Asian amphioxus (B. belcheri), respectively (see Methods). Blan2 corresponds to the latest genome reference for the European amphioxus previous to this publication [8] and Blan3 corresponds to BraLan3, the genome reference for the European amphioxus presented in this...

Additional file 3. Supplementary Note 1.

Additional file 4. Review history.

Additional file 9. Review history.

Additional file 5: Table S4. Non-HhaI amplicons used for cell selection.

Abstract Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration...

Higher adherence to the Mediterranean diet during pregnancy is related to a lower risk of preterm birth and to better offspring cardiometabolic health. DNA methylation may be an underlying biological mechanism. We evaluated whether maternal adherence to the Mediterranean diet was associated with offspring cord blood DNA methylation. We meta-analysed epigenome-wide association studies (EWAS) of maternal adherence to the Mediterranean diet during pregnancy and offspring cord blood DNA methylation in 2802 mother–child pairs from five...

Additional file 1. Supplementary Figures S1-S17.

Additional file 1. Supplementary Figures S1-S17.

Additional file 2: Table S1. Design overview of the panel of targeted regions.

Additional file 4: Table S3. Complete list of CpG methylation-sensitive endonucleases potentially compatible with scTAM-seq.

Additional file 7: Table S6. Doublet detection details per sample and condition.

Abstract Telomere length (TL) is associated with biological aging, consequently influencing the risk of age-related diseases such as Alzheimer’s disease (AD). We aimed to evaluate the potential causal role of TL in AD endophenotypes (i.e., cognitive performance, N = 2233; brain age and AD-related signatures, N = 1134; and cerebrospinal fluid biomarkers (CSF) of AD and neurodegeneration, N = 304) through a Mendelian randomization (MR) analysis. Our analysis was conducted in the context of the...

Additional file 1: Table S1-Table S6.

Additional file 1: Table S1-Table S6.

Additional file 3: Supplementary Table 1. Characteristics of the study participants with information for cognition outcomes. Mean and SD are shown for continuous variables. Supplementary Table 2. Characteristics of the study participants with information for neuroimaging outcomes. Mean and SD are shown for continuous variables. Supplementary Table 3. Characteristics of the study participants with information for CSF biomarkers. Mean and SD are shown for continuous variables.

This folder contains data for "Eighty million years of rapid evolution of the primate Y chromosome" gene_set.zip contains gene annotation (GFF, CDS, PEP, POS.ADD) for the 30 species used in this study XY_location.zip contains the genomic coordinates for PAR, nonPARX and nonPARY (BED format). Species names are in the 4th column. gametolog_alignment.tar.gz contains gametolog alignment (PHY format) used to calculate pairwise dN/dS. S5.tree.zip contains alignment (FASTA format) and constructed phylogeny (NWK format) for each S5...

Abstract This study evaluated the persistence of IgM, IgA, and IgG to SARS-CoV-2 spike and nucleocapsid antigens up to 616 days since the onset of symptoms in a longitudinal cohort of 247 primary health care workers from Barcelona, Spain, followed up since the start of the pandemic. The study also assesses factors affecting antibody levels, including comorbidities and the responses to variants of concern as well as the frequency of reinfections. Despite a gradual and...

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...