A Human-Centered Approach to Measuring the Impact of Evidence-Based Online Resources.

Evidence-based online resources aim to combat vulnerabilities associated with health misinformation, evidence misalignment, and science illiteracy. Yet, it is a challenge to measure and demonstrate their impacts beyond looking at proxies for success (e.g.

The lack of negative association between TE load and subgenome dominance in synthesized allotetraploids.

Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog).

Nursing students' experience of workplace violence in clinical practice: A qualitative systematic review.

Aims: To systematically identify, appraise and synthesise qualitative studies investigating Registered Nurse students' (RNS) experiences of workplace violence (WPV) while on clinical placement. It is expected that the literature review findings will guide the development of targeted programs and policies to address WPV against RNS.

Background: WPV affects RNS during clinical placements as they are vulnerable to violence due to their limited experience and skills to challenge abusive behaviour.

Ovule siRNAs methylate protein-coding genes in trans.

Twenty-four-nucleotide (nt) small interfering RNAs (siRNAs) maintain asymmetric DNA methylation at thousands of euchromatic transposable elements in plant genomes in a process called RNA-directed DNA methylation (RdDM). RdDM is dispensable for growth and development in Arabidopsis thaliana, but is required for reproduction in other plants, such as Brassica rapa. The 24-nt siRNAs are abundant in maternal reproductive tissue, due largely to overwhelming expression from a few loci in the ovule and developing seed coat, termed siren loci.

qTeller: a tool for comparative multi-genomic gene expression analysis.

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses.

Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa.

Background: Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.

Results: Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes.

Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana.

Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype.

Painting a picture of nurse presenteeism: A multi-country integrative review.

Aim: To conduct a review of the impact of presenteeism as it relates to the nursing workforce.

Background: Presenteeism behaviour has been researched in the broader workforce across multiple industries including business/management, public health and occupational health. Presenteeism in nursing is particularly significant because it puts patients at risk by reducing the capacity of nurses to provide high quality care.

Abundant expression of maternal siRNAs is a conserved feature of seed development.

Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In , RdDM is required in the maternal sporophyte for successful seed development.

Author Correction: Origin and evolution of the octoploid strawberry genome.

In the version of this article originally published, author Joshua R. Puzey was incorrectly listed as having affiliation 7 (School of Plant Sciences, University of Arizona, Tucson, AZ, USA); affiliation 6 (Department of Biology, College of William and Mary, Williamsburg, VA, USA) is the correct affiliation. The error has been corrected in the HTML and PDF versions of the article.

Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry.

Gene retention, fractionation and subgenome differences in polyploid plants.

All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality.

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa.

Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.

Natural antisense transcripts are significantly involved in regulation of drought stress in maize.

Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS).

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea.

Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level.

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

Subgenome dominance is an important phenomenon observed in allopolyploids after whole genome duplication, in which one subgenome retains more genes as well as contributes more to the higher expressing gene copy of paralogous genes. To dissect the mechanism of subgenome dominance, we systematically investigated the relationships of gene expression, transposable element (TE) distribution and small RNA targeting, relating to the multicopy paralogous genes generated from whole genome triplication in Brassica rapa. The subgenome dominance was found to be regulated by a relatively stable factor established previously, then inherited by and shared among B.

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences.

A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum.

The pineapple genome and the evolution of CAM photosynthesis.

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit.