Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include ...clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastid-nuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid-nuclear conflict as a novel cause of accelerated evolution.
Asthma in the elderly is underdiagnosed and undertreated, and there is a paucity of knowledge on the subject. The National Institute on Aging convened this workshop to identify what is known and what ...gaps in knowledge remain and suggest research directions needed to improve the understanding and care of asthma in the elderly. Asthma presenting at an advanced age often has similar clinical and physiologic consequences as seen with younger patients, but comorbid illnesses and the psychosocial effects of aging might affect the diagnosis, clinical presentation, and care of asthma in this population. At least 2 phenotypes exist among elderly patients with asthma; those with longstanding asthma have more severe airflow limitation and less complete reversibility than those with late-onset asthma. Many challenges exist in the recognition and treatment of asthma in the elderly. Furthermore, the pathophysiologic mechanisms of asthma in the elderly are likely to be different from those seen in young asthmatic patients, and these differences might influence the clinical course and outcomes of asthma in this population.
The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over ...previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200<E_{ν}^{QE}<1250 MeV. Combining these data with the νover ¯_{e} appearance data from 11.27×10^{20} protons on target in antineutrino mode, a total ν_{e} plus νover ¯_{e} charged-current quasielastic event excess of 460.5±99.0 events (4.7σ) is observed. If interpreted in a two-neutrino oscillation model, ν_{μ}→ν_{e}, the best oscillation fit to the excess has a probability of 21.1%, while the background-only fit has a χ^{2} probability of 6×10^{-7} relative to the best fit. The MiniBooNE data are consistent in energy and magnitude with the excess of events reported by the Liquid Scintillator Neutrino Detector (LSND), and the significance of the combined LSND and MiniBooNE excesses is 6.0σ. A two-neutrino oscillation interpretation of the data would require at least four neutrino types and indicate physics beyond the three neutrino paradigm. Although the data are fit with a two-neutrino oscillation model, other models may provide better fits to the data.
Abstract
Background
In 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.
Results
We 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 in
drdd
mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity.
Conclusions
We 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.
Cosmological observations indicate that most of the matter in the Universe is Dark Matter. Dark Matter in the form of Weakly Interacting Massive Particles (WIMPs) can be detected directly, via its ...elastic scattering off target nuclei. Most current direct detection experiments only measure the energy of the recoiling nuclei. However, directional detection experiments are sensitive to the direction of the nuclear recoil as well. Due to the Sun’s motion with respect to the Galactic rest frame, the directional recoil rate has a dipole feature, peaking around the direction of the Solar motion. This provides a powerful tool for demonstrating the Galactic origin of nuclear recoils and hence unambiguously detecting Dark Matter. Furthermore, the directional recoil distribution depends on the WIMP mass, scattering cross section and local velocity distribution. Therefore, with a large number of recoil events it will be possible to study the physics of Dark Matter in terms of particle and astrophysical properties. We review the potential of directional detectors for detecting and characterizing WIMPs.
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.
Explaining variation in life history strategies is an enduring goal of evolutionary biology and ecology. Early theory predicted that for plants, annual and perennial life histories reflect ...adaptations to environments that experience alternative drought regimens. Nevertheless, empirical support for this hypothesis from comparative analyses remains lacking.
Here, we test classic life history theory in Heliophila L. (Brassicaceae), a diverse genus of flowering plants native to Africa, controlling for phylogeny and integrating 34 yr of satellite-based drought detection with 2192 herbaria occurrence records.
We find that the common ancestor of these species was likely to be an annual, and that perenniality and annuality have repeatedly evolved, an estimated seven and five times, respectively. By comparing historical drought regimens, we show that annuals rather than perennial species occur in environments where droughts are significantly more frequent. We also find evidence that annual plants adapt to predictable drought regimens by escaping drought-prone seasons as seeds.
These results yield compelling support for longstanding theoretical predictions by revealing the importance of drought frequency and predictability to explain plant life history. More broadly, this work highlights scalable approaches, integrating herbaria records and remote sensing to address outstanding questions in evolutionary ecology.
The U.S. Food and Drug Administration (FDA) hopes to achieve greater racial and ethnic diversity in clinical trials, which is urgently needed. 1 As S&P Market Intelligence noted, “The U.S. Food and ...Drug Administration FDA approved a record 59 new therapies in 2018, but among the 53 drugs with U.S. clinical trials, only 12 had enough data to provide some knowledge of the drug's effects across races, the FDA's Drug Trials Snapshots reported. Should we disregard current population shifts and high disparate prevalence rates among Blacks and Latinos who are at least twice as likely (Black/African Americans) or 1.5x as likely (Hispanic/Latinos) as Whites to develop Alzheimer's disease. 4 As a health equity advocate and a person whose father is living with Alzheimer's disease, I find it challenging to applaud a process that tolerates new drugs and therapies being approved based on populations that are not only unrepresentative of the diversity of the U.S. population but also ignores the data pointing to the disparate prevalence of this disease in minority populations. According to the Census Bureau, between 2000 and 2021, the share of the population that is Hispanic/Latino grew the most, increasing 6.2. percentage points to 18.9 %, while the white (non- Hispanic) population had the largest decrease dropping 10.1 percentage points to 59.3%.
Abstract
Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because—like many studies of ...organism-environment interaction—it is primarily informed by experiments considering performance at two discrete levels—wet and dry—rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.
Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly ...understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077–21082. We find that genomic regions enriched in high FST
SNPs colocalize with GT QTL peaks. Many of these high FST
regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST
SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.
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