Musings From a Year of STE[a]M...How It Looks Walking Down the Path

This is a follow up article to one in the inaugural issue which describes the beginnings of implementing a STE[a]M curriculum in a school with a high at-risk student population. This article discusses the outcomes and the future after a year of STE[a]M

Reflections ~ How STEM becomes STEAM

Reflections from designing a STEAM class for high-risk students

What’s Wrong with Interpretive Dance? Embracing the Promise of Integrating the Arts into STEM Learning

Curriculum developers Ruth Catchen and Carolyn DeCristofano explore the benefit and protocol to integrate the arts into STEM

Lost in parameter space: A road map for Stacks

PublishedThis is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1.Restriction site-Associated DNA sequencing (RAD-seq) has become a widely adopted method for genotyping populations of model and non-model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. 2.Using three empirical RAD-seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. 3.Visualisation of the metrics plotted for the three RAD-seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. 4.Our methods will help the community in honing the analytical skills necessary to accurately assemble a RAD-seq dataset.This work was co-funded by the Environment Agency, Westcountry Rivers Trust and the University of Exeter. Overseas collaboration for the project was made possible by funding from The Genetics Society, Santander and the University of Exeter. Thank you to many RAD-seq workshop participants for invaluable insight and new ideas. We thank Dr Nicolas Rochette for his insights into parameter analysis. Thanks also to Dr Andy King for assistance with the brown trout data molecular work and analysis, and Guy Freeman and Martin Young for the species illustrations. Prof Peter Kille and Dr Luis Cunha, Cardiff School of Biosciences, Cardiff University, kindly provided the reference genome of L. rubellus

Anomalous Temperature Dependence of the Electric Field Gradient at the Y Site in In₀.₁Y₀.₉Ba₂Cu₃O\u3csub\u3e9- δ\u3c/sub\u3e

Perturbed angular correlation (PAC) spectroscopy has been used to measure a well-defined static electric quadrupole interaction in a superconducting ceramic, In0.1Y0.9Ba2Cu3O9-δ. Perturbation functions, Fourier transforms, and the derived PAC parameters are given for data taken at temperatures ranging from 77 to 1070 K. Indirect evidence is presented for the occupation of the Y site by the 111In-111Cd PAC probe. The derived electric field gradients were found to increase linearly with temperature. This result suggests the presence of soft, anisotropic vibrations in the structure. Additional evidence is presented to indicate that O2--ion or O-vacancy transport may not occur in the Y coordination sphere

This is What Stem Looks Like! How to Get and Keep Girls Engaged in Science, Technology, Engineering, and Math

Nationally, and in Colorado, the demand for a skilled STEM workforce is growing and STEM jobs offer higher salaries than non-STEM jobs. Women working in STEM jobs earn, on average, 33 percent more than those in other fields, yet women account for only 29 percent of the STEM workforce.  In Colorado, women earn more than 50 percent of two-year and four-year degrees, but less than a third of Colorado graduates in STEM are women.  Women's under-representation in STEM fields starts early, with gender gaps in STEM interests beginning in middle school and growing throughout high school, college, and career. Far too many girls and women are discouraged from pursuing success in STEM fields.We've created this guide to introduce parents, caregivers, and educators to the many opportunities that STEM can provide for girls and women. You'll find resources to help girls explore and prepare for those opportunities and tools to inspire, motivate, and prepare young women to thrive in STEM careers. In addition to tools for creating exciting, hands-on learning experiences, the guide includes: an overview of the status of girls and women in STEM in Colorado, definitions of STEM-related terms, and a call to action. Each chapter includes strategies that are specific to a certain age group, as well as benchmarks to strive for in each stage of girls' lives to prepare them for future STEM opportunities. You might also see some repetition in concepts as they are relevant for girls of many ages. We've included a sampling of the many STEM resources available locally, statewide, and from across the nation

The Impact of Urban Sprawl on Disaster Relief Spending: An Exploratory Study

Students of public policy have written a lot over the years about the rise of suburbia and development beyond older city boundaries in the United States, whether such development has been called urban, suburban, or ex-urban sprawl. Many writers have focused on various issues concerning sprawl, especially on the unintended consequences that new development has had on (among other issues) municipal finances, neighborhood income and residential segregation, and transportation planning. Over the last decade or so, a new area in the literature on sprawl has focused on how the “built-environment” of residential areas can impact health and emergency services. This research note adds to these latest set of papers on sprawl by trying to empirically estimate the impacts of sprawl in metropolitan regions on United States Federal Emergency Management Agency (FEMA) spending on rehabilitating or rebuilding infrastructure in post-disaster relief efforts. In this exploratory analysis the results indicate that urban sprawl is an important factor in influencing FEMA relief spending in the US

Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see if it improves the quality of RAD-Seq markers. Our analyses indicate (1) a modest gap between the number of non-annotated versus annotated SNPs across all species, (2) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs, and (3) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea, and Arabian Gulf with further study. This article is protected by copyright. All rights reserved

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences

Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. We report here the algorithms implemented in Stacks and demonstrate their efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio