Classification of human chronic inflammatory skin disease based on single-cell immune profiling.

Inflammatory conditions represent the largest class of chronic skin disease, but the molecular dysregulation underlying many individual cases remains unclear. Single-cell RNA sequencing (scRNA-seq) has increased precision in dissecting the complex mixture of immune and stromal cell perturbations in inflammatory skin disease states. We single-cell-profiled CD45+ immune cell transcriptomes from skin samples of 31 patients (7 atopic dermatitis, 8 psoriasis vulgaris, 2 lichen planus (LP), 1 bullous pemphigoid (BP), 6 clinical/histopathologically indeterminate rashes, and 7 healthy controls). Our data revealed active proliferative expansion of the Treg and Trm components and universal T cell exhaustion in human rashes, with a relative attenuation of antigen-presenting cells. Skin-resident memory T cells showed the greatest transcriptional dysregulation in both atopic dermatitis and psoriasis, whereas atopic dermatitis also demonstrated recurrent abnormalities in ILC and CD8+ cytotoxic lymphocytes. Transcript signatures differentiating these rash types included genes previously implicated in T helper cell (TH2)/TH17 diatheses, segregated in unbiased functional networks, and accurately identified disease class in untrained validation data sets. These gene signatures were able to classify clinicopathologically ambiguous rashes with diagnoses consistent with therapeutic response. Thus, we have defined major classes of human inflammatory skin disease at the molecular level and described a quantitative method to classify indeterminate instances of pathologic inflammation. To make this approach accessible to the scientific community, we created a proof-of-principle web interface (RashX), where scientists and clinicians can visualize their patient-level rash scRNA-seq-derived data in the context of our TH2/TH17 transcriptional framework.

Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana.

The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.

Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana.

The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana's germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.

Post-Fire Recovery in Coastal Sage Scrub: Seed Rain and Community Trajectory.

Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In this study we considered a variety of mechanisms affecting post-fire vegetation recovery in Riversidean sage scrub. Comparing recently burned plots to unburned plots, we found that burning significantly reduced species richness and percent cover of exotic vegetation the first two years following a 100-hectare wildfire. Seed rain was higher in burned plots, with more native forb seeds, while unburned plots had more exotic grass seeds. Moreover, there were significant correlations between seed rain composition and plant cover composition the year prior and the year after. Collectively, this case study suggests that fire can alter community composition, but there was not compelling evidence of a vegetation-type conversion. Instead, the changes in the community composition were temporary and convergence in community composition was apparent within two years post-fire.

Hydration history and attachment morphology regulate seed release in Chorizanthe rigida (Polygonaceae), a serotinous desert annual.

• Premise of the study: Most seed dispersal studies focus on the spatial aspects of propagule dissemination, i.e., the movement of seeds away from the mother plant. However, the timing of seed release can also be a critical variable influencing the probability of seedling survival. We used a biomechanical approach to analyze seed release in Chorizanthe rigida, a serotinous desert annual, to understand the adaptive significance of seed retention in this species.• Methods: We performed pull-to-break tests on individual propagules (i.e., involucres and achene) from newly developed and older plants, under dry and wet conditions, and recorded the breaking force. We measured the involucral base area using digital images and image processing software.• Key results: There is a positive correlation between the force required to detach an involucre and the size of its base area. The force required to detach involucres from soaked and older plants was lower than that for dry and new plants. This pattern provides a mechanism for the plant to regulate the number of involucres released in different rain events.• Conclusions: Seed release in C. rigida is mediated by propagule morphology, rainfall conditions, and age of the dry plant. These factors allow this species to cope with desert environmental variability by influencing the timing and number of seeds released.

Taxonomic and life history bias in herbicide resistant weeds: implications for deployment of resistant crops.

Evolved herbicide resistance (EHR) is an important agronomic problem and consequently a food security problem, as it jeopardizes herbicide effectiveness and increases the difficulty and cost of weed management. EHR in weeds was first reported in 1970 and the number of cases has accelerated dramatically over the last two decades. Despite 40 years of research on EHR, why some weeds evolve resistance and others do not is poorly understood. Here we ask whether weed species that have EHR are different from weeds in general. Comparing taxonomic and life history traits of weeds with EHR to a control group ("the world's worst weeds"), we found weeds with EHR significantly over-represented in certain plant families and having certain life history biases. In particular, resistance is overrepresented in Amaranthaceae, Brassicaceae and Poaceae relative to all weeds, and annuality is ca. 1.5 times as frequent in weeds with EHR as in the control group. Also, for perennial EHR weeds, vegetative reproduction is only 60% as frequent as in the control group. We found the same trends for subsets of weeds with EHR to acetolactate synthase (ALS), photosystem II (PSII), and 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase-inhibitor herbicides and with multiple resistance. As herbicide resistant crops (transgenic or not) are increasingly deployed in developing countries, the problems of EHR could increase in those countries as it has in the USA if the selecting herbicides are heavily applied and appropriate management strategies are not employed. Given our analysis, we make some predictions about additional species that might evolve resistance.