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Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts (Juglans) and hickories (Carya), show a 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two distinct Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype for female-first flowering inJuglanscontains tandem repeats of the 3′ untranslated region of a gene putatively involved in trehalose-6-phosphate metabolism and is associated with increasedcisgene expression in developing male flowers, possibly mediated by small RNAs. TheCaryalocus contains ~20 syntenic genes and shows molecular signatures of sex chromosome–like evolution. Inheritance mechanisms for heterodichogamy are deeply conserved, yet may occasionally turn over, as in sex determination. 

Abstract BackgroundIn several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear. ResultsWe report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range indrddmutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity. ConclusionsWe propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state. 

Dark matter may induce an event in an Earth-based detector, and its event rate is predicted to show an annual modulation as a result of the Earth’s orbital motion around the Sun. We searched for this modulation signature using the ionization signal of the DarkSide-50 liquid argon time projection chamber. No significant signature compatible with dark matter is observed in the electron recoil equivalent energy range above $40{\mathrm{eV}}_{\mathrm{ee}}$, the lowest threshold ever achieved in such a search. Published by the American Physical Society2024 

Abstract Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases. 

Abstract Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived molecules and activate downstream signaling pathways. We analyzed the variation in NLR gene copy number and identified plants with a low number of NLR genes relative to sister species. We specifically focused on four plants from two distinct lineages, one monocot lineage (Alismatales) and one eudicot lineage (Lentibulariaceae). In these lineages, the loss of NLR genes coincides with loss of the well-known downstream immune signaling complex ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)/PHYTOALEXIN DEFICIENT 4 (PAD4). We expanded our analysis across whole proteomes and found that other characterized immune genes were absent only in Lentibulariaceae and Alismatales. Additionally, we identified genes of unknown function that were convergently lost together with EDS1/PAD4 in five plant species. Gene expression analyses in Arabidopsis (Arabidopsis thaliana) and Oryza sativa revealed that several homologs of the candidates are differentially expressed during pathogen infection, drought, and abscisic acid treatment. Our analysis provides evolutionary evidence for the rewiring of plant immunity in some plant lineages, as well as the coevolution of the EDS1/PAD4 pathway and drought responses. 

Abstract The DarkSide-20k dark matter experiment, currently under construction at LNGS, features a dual-phase time projection chamber (TPC) with a ∼ 50 t argon target from an underground well. At this scale, it is crucial to optimise the argon flow pattern for efficient target purification and for fast distribution of internal gaseous calibration sources with lifetimes of the order of hours. To this end, we have performed computational fluid dynamics simulations and heat transfer calculations. The residence time distribution shows that the detector is well-mixed on time-scales of the turnover time (∼ 40 d). Notably, simulations show that despite a two-order-of-magnitude difference between the turnover time and the half-life of^83mKr of 1.83 h, source atoms have the highest probability to reach the centre of the TPC 13 min after their injection, allowing for a homogeneous distribution before undergoing radioactive decay. We further analyse the thermal aspects of dual-phase operation and define the requirements for the formation of a stable gas pocket on top of the liquid. We find a best-estimate value for the heat transfer rate at the liquid-gas interface of 62 W with an upper limit of 144 W and a minimum gas pocket inlet temperature of 89 K to avoid condensation on the acrylic anode. This study also informs the placement of liquid inlets and outlets in the TPC. The presented techniques are widely applicable to other large-scale, noble-liquid detectors. 

Abstract DarkSide-20k is a novel liquid argon dark matter detector currently under construction at the Laboratori Nazionali del Gran Sasso (LNGS) of the Istituto Nazionale di Fisica Nucleare (INFN) that will push the sensitivity for Weakly Interacting Massive Particle (WIMP) detection into the neutrino fog. The core of the apparatus is a dual-phase Time Projection Chamber (TPC), filled with 50 tonnes of low radioactivity underground argon (UAr) acting as the WIMP target. NUV-HD-cryo Silicon Photomultipliers (SiPM)s designed by Fondazione Bruno Kessler (FBK) (Trento, Italy) were selected as the photon sensors covering two$$10.5~\text {m}^2$$ $10.5{\text{m}}^2$Optical Planes, one at each end of the TPC, and a total of$$5~\text {m}^2$$ $5{\text{m}}^2$photosensitive surface for the liquid argon veto detectors. This paper describes the Quality Assurance and Quality Control (QA/QC) plan and procedures accompanying the production of FBK NUV-HD-cryo SiPM wafers manufactured by LFoundry s.r.l. (Avezzano, AQ, Italy). SiPM characteristics are measured at 77 K at the wafer level with a custom-designed probe station. As of March 2025, 1314 of the 1400 production wafers (94% of the total) for DarkSide-20k were tested. The wafer yield is$$93.2\pm 2.5$$ $93.2\pm 2.5$%, which exceeds the 80% specification defined in the original DarkSide-20k production plan.