Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize

Many transposable elements in maize alternate between active and inactive phases associated with the modification of their DNA. Elements in an inactive phase lose their ability to transpose, their ability to excise from reporter alleles and, in some cases, their ability to enhance or suppress mutant phenotypes caused by their insertion. The maize mutant hcf106 is a recessive pale green seedling lethal caused by the insertion of the transposable element Mu1. We show that the hcf106 mutant phenotype is suppressed in lines that have lost Mu activity. That is, homozygous hcf106 seedlings are dark green and viable when transposable elements belonging to the Robertson's Mutator family are modified in their terminal inverted repeats, a diagnostic feature of inactive lines. This property of the mutant phenotype has been used to follow clonal leaf sectors containing modified Mu elements that arise from single somatic cells during plant development. The distribution of these sectors indicates that epigenetic switches involving Mu DNA modification occur progressively as the meristem ages

First Record of the Plains Minnow, Hybognathus placitus, in Canada

Seven Plains Minnows, Hybognathus placitus, Family Cyprinidae, were collected on 11 June 2003 from Morgan Creek, in Grasslands National Park, Saskatchewan, Canada. This collection is the first record of the species in Canada and extends the northern distribution limit of the species. Of 95 Hybognathus spp. collected at the site, only eight specimens were retained for positive identification because of the uncertain status of two conspecifics, the Western Silvery Minnow, H. argyritis, and the Brassy Minnow, H. hankinsoni, in Saskatchewan. Our findings should stimulate additional sampling to assess the identification and status of Hybognathus spp. in southwestern Saskatchewan. Accurate field identification of Hybognathus spp. remains an issue and collection of all specimens is recommended to accurately identify members within the genus

Functional interplay between chromatin remodeling complexes RSC, SWI/SNF and ISWI in regulation of yeast heat shock genes

Chromatin remodeling is an essential part of transcription initiation. We show that at heat shock gene promoters functional interactions between individual ATP-dependent chromatin remodeling complexes play critical role in both nucleosome displacement and Pol II recruitment. Using HSP12, HSP82 and SSA4 gene promoters as reporters, we demonstrated that while inactivation of SNF2, a critical ATPase of the SWI/SNF complex, primarily affects the HSP12 promoter, depletion of STH1- a SNF2 homolog from the RSC complex reduces histone displacement and abolishes the Pol II recruitment at all three promoters. From these results, we conclude that redundancy between SWI/SNF and RSC complexes is only partial and likely is affecting different chromatin remodeling steps. While inactivation of other individual ATP-dependent chromatin remodeling complexes negligibly affects reporter promoters, combinatorial inactivation of SNF2 and ISW1 has a synergistic effect by diminishing histone loss during heat induction and eliminating Pol II recruitment. Importantly, it also eliminates preloading of HSF on HSP82 and SSA4 promoters before heat shock and diminishes HSF binding during heat shock. These observations suggest that prior action of chromatin remodeling complexes is necessary for the activator binding

How the vertebrates were made: selective pruning of a double-duplicated genome

Vertebrates are the result of an ancient double duplication of the genome. A new study published in BMC Biology explores the selective retention of genes after this event, finding an extensive enrichment of signaling proteins and transcription factors. Analysis of their expression patterns, interactions and subsequent history reflect the forces that drove their evolution, and with it the evolution of vertebrate complexity

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

Following genome duplication and selfish DNA expansion, maize used a heretofore unknown mechanism to shed redundant genes and functionless DNA with bias toward one of the parental genomes

Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats

Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition

Better writing in scientific publications builds reader confidence and understanding

Scientific publications are the building blocks of discovery and collaboration, but their impact is limited by the style in which they are traditionally written. Recently, many authors have called for a switch to an engaging, accessible writing style. Here, we experimentally test how readers respond to such a style. We hypothesized that scientific abstracts written in a more accessible style would improve readers’ reported readability and confidence as well as their understanding, assessed using multiple-choice questions on the content. We created a series of scientific abstracts, corresponding to real publications on three scientific topics at four levels of difficulty – varying from the difficult, traditional style to an engaging, accessible style. We gave these abstracts to a team of readers consisting of 170 third-year undergraduate students. Then, we posed questions to measure the readers’ readability, confidence, and understanding with the content. The scientific abstracts written in a more accessible style resulted in higher readability, understanding, and confidence. These findings demonstrate that rethinking the way we communicate our science may empower a more collaborative and diverse industry.Benjamin S. Freeling, Zoë A. Doubleday, Matthew J. Dry, Carolyn Semmler and Sean D. Connel

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. Results: To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms’ databases. Availability and implementation: The source code for qTeller is open-source and available through GitHub (https:// github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes