The epigenetic basis of cellular heterogeneity.

Single-cell sequencing-based methods for profiling gene transcript levels have revealed substantial heterogeneity in expression levels among morphologically indistinguishable cells. This variability has important functional implications for tissue biology and disease states such as cancer. Mapping of epigenomic information such as chromatin accessibility, nucleosome positioning, histone tail modifications and enhancer-promoter interactions in both bulk-cell and single-cell samples has shown that these characteristics of chromatin state contribute to expression or repression of associated genes. Advances in single-cell epigenomic profiling methods are enabling high-resolution mapping of chromatin states in individual cells. Recent studies using these techniques provide evidence that variations in different aspects of chromatin organization collectively define gene expression heterogeneity among otherwise highly similar cells.

Contribution of the histone variant H2A.Z to expression of responsive genes in plants.

The histone variant H2A.Z plays a critical role in chromatin-based processes such as transcription, replication, and repair in eukaryotes. Although many H2A.Z-associated processes and features are conserved in plants and animals, a distinguishing feature of plant chromatin is the enrichment of H2A.Z in the bodies of genes that exhibit dynamic expression, particularly in response to differentiation and the environment. Recent work sheds new light on the plant machinery that enables dynamic changes in H2A.Z enrichment and identifies additional chromatin-based pathways that contribute to transcriptional properties of H2A.Z-enriched chromatin. In particular, analysis of a variety of responsive loci reveals a repressive role for H2A.Z in expression of responsive genes and identifies roles for SWR1 and INO80 chromatin remodelers in enabling dynamic regulation of H2A.Z levels and transcription. These studies lay the groundwork for understanding how this ancient histone variant is harnessed by plants to enable responsive and dynamic gene expression (Graphical Abstract).

Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates.

Most organophosphates (OPs) are hydrophobic, and after exposure, can sequester into lipophilic regions within the body, such as adipose tissue, resulting in long term chronic effects. Consequently, there is an urgent need for therapeutic agents that can decontaminate OPs in these hydrophobic regions. Accordingly, an enzyme-polymer surfactant nanocomplex is designed and tested comprising chemically supercharged phosphotriesterase (Agrobacterium radiobacter; arPTE) electrostatically conjugated to amphiphilic polymer surfactant chains ([cat.arPTE][S-]). Experimentally-derived structural data are combined with molecular dynamics (MD) simulations to provide atomic level detail on conformational ensembles of the nanocomplex using dielectric constants relevant to aqueous and lipidic microenvironments. These show the formation of a compact admicelle pseudophase surfactant corona under aqueous conditions, which reconfigures to yield an extended conformation at a low dielectric constant, providing insight into the mechanism underpinning cell membrane binding. Significantly, it demonstrated that [cat.arPTE][S-] spontaneously binds to human mesenchymal stem cell membranes (hMSCs), resulting in on-cell OP hydrolysis. Moreover, the nanoconstruct can endocytose and partition into the intracellular fatty vacuoles of adipocytes and hydrolyze sequestered OP.

Moss functional trait ecology: Trends, gaps, and biases in the current literature.

Functional traits are critical tools in plant ecology for capturing organism-environment interactions based on trade-offs and making links between organismal and ecosystem processes. While broad frameworks for functional traits have been developed for vascular plants, we lack the same for bryophytes, despite an escalation in the number of studies on bryophyte functional trait in the last 45 years and an increased recognition of the ecological roles bryophytes play across ecosystems. In this review, we compiled data from 282 published articles (10,005 records) that focused on functional traits measured in mosses and sought to examine trends in types of traits measured, capture taxonomic and geographic breadth of trait coverage, reveal biases in coverage in the current literature, and develop a bryophyte-function index (BFI) to describe the completeness of current trait coverage and identify global gaps to focus research efforts. The most commonly measured response traits (those related to growth/reproduction in individual organisms) and effect traits (those that directly affect community/ecosystem scale processes) fell into the categories of morphology (e.g., leaf area, shoot height) and nutrient storage/cycling, and our BFI revealed that these data were most commonly collected from temperate and boreal regions of Europe, North America, and East Asia. However, fewer than 10% of known moss species have available functional trait information. Our synthesis revealed a need for research on traits related to ontogeny, sex, and intraspecific plasticity and on co-measurement of traits related to water relations and bryophyte-mediated soil processes.

Development of Neighborhood Trajectories Employing Historic Redlining and the Area Deprivation Index.

The role of historic residential redlining on health inequities is intertwined with policy changes made before and after the 1930s that influence current neighborhood characteristics and shape ongoing structural racism in the United States (U.S.). We developed Neighborhood Trajectories which combine historic redlining data and the current neighborhood socioeconomic characteristics as a novel approach to studying structural racism. Home Owners' Loan Corporation (HOLC) neighborhoods for the entire U.S. were used to map the HOLC grades to the 2020 U.S. Census block group polygons based on the percentage of HOLC areas in each block group. Each block group was also assigned an Area Deprivation Index (ADI) from the Neighborhood Atlas®. To evaluate changes in neighborhoods from historic HOLC grades to present degree of deprivation, we aggregated block groups into "Neighborhood Trajectories" using historic HOLC grades and current ADI. The Neighborhood Trajectories are "Advantage Stable"; "Advantage Reduced"; "Disadvantage Reduced"; and "Disadvantage Stable." Neighborhood Trajectories were established for 13.3% (32,152) of the block groups in the U.S., encompassing 38,005,799 people. Overall, the Disadvantage-Reduced trajectory had the largest population (16,307,217 people). However, the largest percentage of non-Hispanic/Latino Black residents (34%) fell in the Advantage-Reduced trajectory, while the largest percentage of Non-Hispanic/Latino White residents (60%) fell in the Advantage-Stable trajectory. The development of the Neighborhood Trajectories affords a more nuanced mechanism to investigate dynamic processes from historic policy, socioeconomic development, and ongoing marginalization. This adaptable methodology may enable investigation of ongoing sociopolitical processes including gentrification of neighborhoods (Disadvantage-Reduced trajectory) and "White flight" (Advantage Reduced trajectory).

Residential Redlining, Neighborhood Trajectory, and Equity of Breast and Colorectal Cancer Care.

OBJECTIVE: This study aimed to determine the influence of structural racism, vis-à-vis neighborhood socioeconomic trajectory, on colorectal and breast cancer diagnosis and treatment. SUMMARY BACKGROUND DATA: Inequities in cancer care are well documented in the United States but less is understood about how historical policies like residential redlining and evolving neighborhood characteristics influence current gaps in care. METHODS: This retrospective cohort study included adult patients diagnosed with colorectal or breast cancer between 2010 and 2015 in 7 Indiana cities with available historic redlining data. Current neighborhood socioeconomic status was determined by the Area Deprivation Index (ADI). Based on historic redlining maps and current ADI, we created four "Neighborhood Trajectory" categories: Advantage Stable, Advantage Reduced, Disadvantage Stable, Disadvantage Reduced. Modified Poisson regression models estimated the relative risks (RR) of Neighborhood Trajectory on cancer stage at diagnosis and receipt of cancer-directed surgery (CDS). RESULTS: A final cohort derivation identified 4,862 cancer patients with colorectal or breast cancer. Compared to Advantage Stable neighborhoods, Disadvantage Stable neighborhood was associated with late-stage diagnosis for both colorectal and breast cancer (RR=1.30 [95% CI=1.05 - 1.59]; RR=1.41 [1.09 - 1.83], respectively). Black patients had lower likelihood of receiving CDS in Disadvantage Reduced neighborhoods (RR=0.92 [0.86 - 0.99]) than White patients. CONCLUSIONS: Disadvantage Stable neighborhoods were associated with late-stage diagnosis for breast and colorectal cancer. Disadvantage Reduced (gentrified) neighborhoods were associated with racial-inequity in CDS. Improved neighborhood socioeconomic conditions may improve timely diagnosis but could contribute to racial inequities in surgical treatment.

Parallel evolution and cryptic diversification in a common and widespread Amazonian tree, Protium subserratum.

The lowland Amazon rainforest houses some of the greatest tree diversity on Earth. While the vast majority of these species are rare, a small number are common and widespread and thus considered to play a disproportionate role in many of the global ecosystem services provided by the Amazon. However, the extent to which dominant Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring within Protium subserratum (Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with soil and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range, we found that P. subserratum contains at least eight distinct clades. Specialization onto white-sand soils has evolved independently at least twice within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazon tree species may not represent evolutionary cohesive units. Instead, these dominant species may more commonly represent species complexes, undergoing evolutionary transitions on a trajectory to become multiple range-restricted, specialist species.

Implementation of an interprofessional education program in a community teaching hospital and its impact on student perceptions of other healthcare professions.

In this single-center, prospective study we evaluated the impact of an interprofessional education program (IPE) on healthcare students' perceptions of other healthcare professions. The program consisted of four one-hour, roundtable, case-based sessions with students and several facilitators from medicine, nursing, pharmacy, and physician assistant programs. Included students were 18 years of age or older and currently enrolled in a healthcare program during the study time frame. The primary outcome of student perceptions of other healthcare professions was measured by baseline and follow-up surveys using the Adapted Attitudes Toward Interprofessional Health Care Teams scale. Perceptions of students who participated in the IPEP (intervention group) were compared to similar healthcare program students who did not participate in the program (control group). Overall, the intervention group had significantly higher perceptions of other healthcare professions comparing pre-intervention to post -intervention data (pre-intervention mean ± SD of 57.2 ± 5.24; post-intervention mean 60.7 ± 5.63; p = .02). This improvement in perceptions was also seen when comparing the post-intervention group to the control group (control mean 56.7 ± 5.1; post-intervention mean 60.7 ± 5.63; p = .008).

Overexpression of arogenate dehydratase reveals an upstream point of metabolic control in phenylalanine biosynthesis.

Out of the three aromatic amino acids, the highest flux in plants is directed towards phenylalanine, which is utilized to synthesize proteins and thousands of phenolic metabolites contributing to plant fitness. Phenylalanine is produced predominantly in plastids via the shikimate pathway and subsequent arogenate pathway, both of which are subject to complex transcriptional and post-transcriptional regulation. Previously, it was shown that allosteric feedback inhibition of arogenate dehydratase (ADT), which catalyzes the final step of the arogenate pathway, restricts flux through phenylalanine biosynthesis. Here, we show that in petunia (Petunia hybrida) flowers, which typically produce high phenylalanine levels, ADT regulation is relaxed, but not eliminated. Moderate expression of a feedback-insensitive ADT increased flux towards phenylalanine, while high overexpression paradoxically reduced phenylalanine formation. This reduction could be partially, but not fully, recovered by bypassing other known metabolic flux control points in the aromatic amino acid network. Using comparative transcriptomics, reverse genetics, and metabolic flux analysis, we discovered that transcriptional regulation of the d-ribulose-5-phosphate 3-epimerase gene in the pentose phosphate pathway controls flux into the shikimate pathway. Taken together, our findings reveal that regulation within and upstream of the shikimate pathway shares control over phenylalanine biosynthesis in the plant cell.

Integrating web applications into popular survey platforms for online experiments.

Research using custom-made web applications is burgeoning as scholars increasingly conduct their experiments online. We show how researchers can integrate their web applications into popular survey software such as Qualtrics in five simple steps and provide the full JavaScript code and screenshots. This procedure allows participants to seamlessly switch from Qualtrics to their web applications without leaving the survey platform. This integration has two benefits: (1) it eliminates the risk that participants inadvertently drop out of the survey while switching from the survey software to the web application and vice versa; and (2) it saves researchers the fees charged by survey companies to host an external link on the survey platform. Hence, we make it easier to conduct research on targeted (e.g., national) samples using web applications.

The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis.

Selective, tissue-specific gene expression is facilitated by the epigenetic modification H3K27me3 (trimethylation of lysine 27 on histone H3) in plants and animals. Much remains to be learned about how H3K27me3-enriched chromatin states are constructed and maintained. Here, we identify a genetic interaction in Arabidopsis thaliana between the chromodomain helicase DNA binding chromatin remodeler PICKLE (PKL), which promotes H3K27me3 enrichment, and the SWR1-family remodeler PHOTOPERIOD INDEPENDENT EARLY FLOWERING1 (PIE1), which incorporates the histone variant H2A.Z. Chromatin immunoprecipitation-sequencing and RNA-sequencing reveal that PKL, PIE1, and the H3K27 methyltransferase CURLY LEAF act in a common gene expression pathway and are required for H3K27me3 levels genome-wide. Additionally, H3K27me3-enriched genes are largely a subset of H2A.Z-enriched genes, further supporting the functional linkage between these marks. We also found that recombinant PKL acts as a prenucleosome maturation factor, indicating that it promotes retention of H3K27me3. These data support the existence of an epigenetic pathway in which PIE1 promotes H2A.Z, which in turn promotes H3K27me3 deposition. After deposition, PKL promotes retention of H3K27me3 after DNA replication and/or transcription. Our analyses thus reveal roles for H2A.Z and ATP-dependent remodelers in construction and maintenance of H3K27me3-enriched chromatin in plants.

Isomorphs in nanoconfined liquids.

We study in this paper the possible existence of Roskilde-simple liquids and their isomorphs in a rough-wall nanoconfinement. Isomorphs are curves in the thermodynamic phase diagram along which structure and dynamics are invariant in suitable nondimensionalized units. Two model liquids using molecular dynamics computer simulations are considered: the single-component Lennard-Jones (LJ) liquid and the Kob-Andersen binary LJ mixture, both of which in the bulk phases are known to have good isomorphs. Nanoconfinement is implemented by adopting a slit-pore geometry with fcc crystalline walls; this implies inhomogenous density profiles both parallel and perpendicular to the confining walls. Despite this fact and consistent with an earlier study [Ingebrigtsen et al., Phys. Rev. Lett., 2013, 111, 235901] we find that these two nanoconfined liquids have isomorphs to a good approximation. More specifically, we show good invariance along the isomorphs of inhomogenous density profiles, mean-square displacements, and higher-order structures probed using the topological cluster classification algorithm. Our study thus provides an alternative framework for understanding nanoconfined liquids.

The roles of dispersal limitation, climatic niches and glacial history in endemism of the North American bryophyte flora.

PREMISE: Bryophytes (mosses, liverworts, and hornworts) tend to have very large geographic ranges, which impedes progress toward understanding the drivers of diversification and extinction. This study aimed to investigate whether North American endemics differ geographically from more widespread species and whether differences in climatic niche or traits related to dispersal and establishment differ between endemics and more widespread species. METHODS: All available herbarium records of bryophytes from North America north of Mexico (106 collections) were used. Traits related to dispersal were obtained from the literature. Analyses tested whether range sizes and extents differed between endemics and nonendemics, and whether trait differences were associated with endemism. Climate data were used to determine whether differences in niche breadth are present between endemics and nonendemics, and whether suitable climate for endemics occurs outside North America. RESULTS: Nonendemics have range sizes twice as large as endemics and they occur farther north and have greater longitudinal extents. However, they do not have the widest niche breadths and do not differ in spore size (with few exceptions) or sexual condition. Asexual propagules are more prevalent among nonendemics. Climatic models indicate that substantial areas of climate suitable for endemics exist outside of North America. CONCLUSIONS: Distributions of endemics and nonendemics are consistent with an important role of glaciation in shaping the North American bryophyte flora. Endemics are not limited to the continent based on a lack of suitable climate elsewhere or by spore size or sexual condition.

Isomorph Invariance of Higher-Order Structural Measures in Four Lennard-Jones Systems.

In the condensed liquid phase, both single- and multicomponent Lennard-Jones (LJ) systems obey the "hidden-scale-invariance" symmetry to a good approximation. Defining an isomorph as a line of constant excess entropy in the thermodynamic phase diagram, the consequent approximate isomorph invariance of structure and dynamics in appropriate units is well documented. However, although all measures of the structure are predicted to be isomorph invariant, with few exceptions only the radial distribution function (RDF) has been investigated. This paper studies the variation along isomorphs of the nearest-neighbor geometry quantified by the occurrence of Voronoi structures, Frank-Kasper bonds, icosahedral local order, and bond-orientational order. Data are presented for the standard LJ system and for three binary LJ mixtures (Kob-Andersen, Wahnström, NiY2). We find that, while the nearest-neighbor geometry generally varies significantly throughout the phase diagram, good invariance is observed along the isomorphs. We conclude that higher-order structural correlations are no less isomorph invariant than is the RDF.

Linguistic networks associated with lexical, semantic and syntactic predictability in reading: A fixation-related fMRI study.

The ability to make predictions is thought to facilitate language processing. During language comprehension such predictions appear to occur at multiple levels of linguistic representations (i.e. semantic, syntactic and lexical). The neural mechanisms that define the network sensitive to linguistic predictability have yet to be adequately defined. The purpose of the present study was to explore the neural network underlying predictability during the normal reading of connected text. Predictability values for different linguistic information were obtained from a pre-existing text corpus. Forty-one subjects underwent simultaneous eye-tracking and fMRI scans while reading these select paragraphs. Lexical, semantic, and syntactic predictability measures were then correlated with functional activation associated with fixation onset on the individual words. Activation patterns showed both positive and negative correlations to lexical, semantic, and syntactic predictabilities. Conjunction analysis revealed regions specific to or shared between each type of predictability. The regions associated with the different predictability measures were largely separate. Results suggest that most linguistic predictions are graded in nature, activating components of the existing language system. A number of regions were also found to be uniquely associated with full lexical predictability, most notably the anterior temporal lobe and the inferior posterior temporal cortex.

Sequential Electrostatic Assembly of a Polymer Surfactant Corona Increases Activity of the Phosphotriesterase arPTE.

We present a new methodology for the generation of discrete molecularly dispersed enzyme-polymer-surfactant bioconjugates. Significantly, we demonstrate that >3-fold increase in the catalytic efficiency of the diffusion-limited phosphotriesterase arPTE can be achieved through sequential electrostatic addition of cationic and anionic polymer surfactants, respectively. Here, the polymer surfactants assemble on the surface of the enzyme via ion exchange to yield a compact corona. The observed rate enhancement is consistent with a mechanism whereby the polymer-surfactant corona gives rise to a decrease in the dielectric constant in the vicinity of the active site of the enzyme, accelerating the rate-determining product diffusion step. The facile methodology has significant potential for increasing the efficiency of enzymes and could therefore have a substantially positive impact for industrial enzymology.

Range change evolution of peat mosses (Sphagnum) within and between climate zones.

Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat-forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool-or cold-climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates.

Structural covariance in the hard sphere fluid.

We study the joint variability of structural information in a hard sphere fluid biased to avoid crystallisation and form five-fold symmetric geometric motifs. We show that the structural covariance matrix approach, originally proposed for on-lattice liquids [P. Ronceray and P. Harrowell, J. Stat. Mech.: Theory Exp. 2016(8), 084002], can be meaningfully employed to understand structural relationships between different motifs and can predict, within the linear-response regime, structural changes related to motifs distinct from that used to bias the system.

Perturbation of H3K27me3-Associated Epigenetic Processes Increases Agrobacterium-Mediated Transformation.

Agrobacterium-mediated transformation is a core technology for basic plant science and agricultural biotechnology. Improving transformation frequency is a major goal for plant transgenesis. We previously showed that T-DNA insertions in some histone genes decreased transformation susceptibility, whereas overexpression of several Arabidopsis H2A and H4 isoforms increased transformation. Overexpression of several histone H2B and H3 isoforms had little effect on transformation frequency. However, overexpression of histone H3-11 (HTR11) enhanced transformation. HTR11 is a unique H3 variant that lacks lysine at positions 9 and 27. The modification status of these lysine residues in canonical H3 proteins plays a critical role in epigenetic determination of gene expression. We mutated histone H3-4 (HTR4), a canonical H3.3 protein that does not increase transformation when overexpressed, by replacing either or both K9 and K27 with the amino acids in HTR11 (either K9I, K27Q, or both). Overexpression of HTR4 with the K27Q but not the K9I substitution enhanced transformation. HTR4K27Q was incorporated into chromatin, and HTR4K27Q overexpression lines exhibited deregulated expression of H3K27me3-enriched genes. These results demonstrate that mutation of K27 in H3.3 is sufficient to perturb H3K27me3-dependent expression in plants as in animals and suggest a distinct epigenetic role for histone HTR11. Further, these observations implicate manipulation of H3K27me3-dependent gene expression as a novel strategy to increase transformation susceptibility.

Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta).

Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.