Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis

Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and ultrahigh-performance liquid chromatography (UHPLC), we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5‐methylcytosine (5mC), is the main DNA methylation mark in T. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain superfamilies of DNA transposable elements. We show that 6mA in T. vaginalis is associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions, and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a role for 6mA in modulating three-dimensional (3D) chromatin structure and gene expression in this divergent member of the Excavata.Fil: Lizarraga, Ayelen. Universidad Nacional de San Martin. Instituto Tecnologico de Chascomus. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - la Plata. Instituto Tecnologico de Chascomus.; ArgentinaFil: O'Brown, Zach Klapholz. Harvard Medical School; Estados UnidosFil: Boulias, Konstantinos. Harvard Medical School; Estados UnidosFil: Roach, Lara. Harvard Medical School; Estados UnidosFil: Greer, Eric Lieberman. Harvard Medical School; Estados UnidosFil: Johnson, Patricia J.. University of California at Los Angeles; Estados UnidosFil: Strobl Mazzulla, Pablo H.. Universidad Nacional de San Martin. Instituto Tecnologico de Chascomus. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - la Plata. Instituto Tecnologico de Chascomus.; ArgentinaFil: de Miguel, Natalia. Universidad Nacional de San Martin. Instituto Tecnologico de Chascomus. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - la Plata. Instituto Tecnologico de Chascomus.; Argentin

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (, , ) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types

Post-Franco Theatre

In the multiple realms and layers that comprise the contemporary Spanish theatrical landscape, “crisis” would seem to be the word that most often lingers in the air, as though it were a common mantra, ready to roll off the tongue of so many theatre professionals with such enormous ease, and even enthusiasm, that one is prompted to wonder whether it might indeed be a miracle that the contemporary technological revolution – coupled with perpetual quandaries concerning public and private funding for the arts – had not by now brought an end to the evolution of the oldest of live arts, or, at the very least, an end to drama as we know it

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Optimisation and Validation of a Nutritional Intervention to Enhance Sleep Quality and Quantity.

Disturbed sleep may negatively influence physical health, cognitive performance, metabolism, and general wellbeing. Nutritional interventions represent a potential non-pharmacological means to increase sleep quality and quantity. (1) Identify an optimal suite of nutritional ingredients and (2) validate the effects of this suite utilising polysomnography, and cognitive and balance tests. The optimal and least optimal combinations of six ingredients were identified utilising 55 male participants and a Box-Behnken predictive model. To validate the model, 18 healthy, male, normal sleepers underwent three trials in a randomised, counterbalanced design: (1) optimal drink, (2) least optimal drink, or (3) placebo were provided before bed in a double-blinded manner. Polysomnography was utilised to measure sleep architecture. Cognitive performance, postural sway, and subjective sleep quality, were assessed 30 min after waking. The optimal drink resulted in a significantly shorter sleep onset latency (9.9 ± 12.3 min) when compared to both the least optimal drink (26.1 ± 37.4 min) and the placebo drink (19.6 ± 32.0 min). No other measures of sleep, cognitive performance, postural sway, and subjective sleep quality were different between trials. A combination of ingredients, optimised to enhance sleep, significantly reduced sleep onset latency. No detrimental effects on sleep architecture, subjective sleep quality or next day performance were observed

Optimisation and validation of a nutritional intervention to enhance sleep quality and quantity

Sargent, C ORCiD: 0000-0001-5340-4701BACKGROUND: Disturbed sleep may negatively influence physical health, cognitive performance, metabolism, and general wellbeing. Nutritional interventions represent a potential non-pharmacological means to increase sleep quality and quantity. OBJECTIVE: (1) Identify an optimal suite of nutritional ingredients and (2) validate the effects of this suite utilising polysomnography, and cognitive and balance tests. METHODS: The optimal and least optimal combinations of six ingredients were identified utilising 55 male participants and a Box-Behnken predictive model. To validate the model, 18 healthy, male, normal sleepers underwent three trials in a randomised, counterbalanced design: (1) optimal drink, (2) least optimal drink, or (3) placebo were provided before bed in a double-blinded manner. Polysomnography was utilised to measure sleep architecture. Cognitive performance, postural sway, and subjective sleep quality, were assessed 30 min after waking. RESULTS: The optimal drink resulted in a significantly shorter sleep onset latency (9.9 ± 12.3 min) when compared to both the least optimal drink (26.1 ± 37.4 min) and the placebo drink (19.6 ± 32.0 min). No other measures of sleep, cognitive performance, postural sway, and subjective sleep quality were different between trials. CONCLUSION: A combination of ingredients, optimised to enhance sleep, significantly reduced sleep onset latency. No detrimental effects on sleep architecture, subjective sleep quality or next day performance were observed