More Like this

1. Choosing your own adventure: Engaging the new learning society through integrative curriculum design

   https://doi.org/10.29007/567f  

   Ryder, Elizabeth; Ruiz, Carolina; Weaver, Shari; Gegear, Robert (February 2020, EPiC Series in Education Science)

   In our increasingly data-driven society, it is critical for high school students to learn to integrate computational thinking with other disciplines in solving real world problems. To address this need for the life sciences in particular, we have developed the Bio-CS Bridge, a modular computational system coupled with curriculum integrating biology and computer science. Our transdisciplinary team comprises university and high school faculty and students with expertise in biology, computer science, and education. Our approach engages students and teachers in scientific practices using biological data that they can collect themselves, and computational tools that they help to design and implement, to address the real-world problem of pollinator decline. Our modular approach to high school curriculum design provides teachers with the educational flexibility to address national and statewide biology and computer science standards for a wide range of learner types. We are using a teacher- leader model to disseminate the Bio-CS Bridge, whose components will be freely available online. 

   more » « less
2. Exploring FlyBase Data Using QuickSearch

   https://doi.org/10.1002/cpz1.731  

   Marygold, Steven J.; the FlyBase Consortium (April 2023, Current Protocols)

   Abstract FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch Basic Protocol 2: Using the “Data Class” tab of QuickSearch Basic Protocol 3: Using the “References” tab of QuickSearch Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch Basic Protocol 5: Using the “Pathways” tab of QuickSearch Basic Protocol 6: Using the “GO” tab of QuickSearch Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch Basic Protocol 8: Using the “Expression” tab of QuickSearch Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch Basic Protocol 10: Using the “Phenotype” tab of QuickSearch Basic Protocol 11: Using the “Human Disease” tab of QuickSearch Basic Protocol 12: Using the “Homologs” tab of QuickSearch Support Protocol 1: Managing FlyBase hit lists 

   more » « less
3. Birds are not the only ones impacted by guidance to cease bird feeding

   https://doi.org/10.1002/pan3.10566  

   Dayer, Ashley A.; Pototsky, P. Christy; Hall, Richard J.; Hawley, Dana M.; Phillips, Tina B.; Bonter, David N.; Dietsch, Alia M.; Greig, Emma; Hochachka, Wesley M. (December 2023, People and Nature)

   Abstract Humans have a particularly strong connection with birds, driving the enormous popularity of residential bird feeding in much of the world.We conducted a web search to document US state wildlife management agency responses to two recent avian disease outbreaks, finding that 23 agencies made recommendations to cease feeding wild birds in 2021–2022.The psychological benefits of bird feeding for humans are well‐documented but often overlooked in management decisions in response to avian disease outbreaks.Likewise, ecological evidence does not necessarily support ceasing bird feeding to reduce the spread of every avian disease.Ecological and social science need to be applied in tandem to ensure that well‐intended guidance to cease feeding of birds does not have unintended consequences. 

   more » « less
4. Quantifying Soil Phosphorus Dynamics: A Data Assimilation Approach

   https://doi.org/10.1029/2018JG004903  

   Hou, Enqing; Lu, Xingjie; Jiang, Lifen; Wen, Dazhi; Luo, Yiqi (July 2019, Journal of Geophysical Research: Biogeosciences)

   Abstract The dynamics of soil phosphorus (P) control its bioavailability. Yet it remains a challenge to quantify soil P dynamics. Here we developed a soil P dynamics (SPD) model. We then assimilated eight data sets of 426‐day changes in Hedley P fractions into the SPD model, to quantify the dynamics of six major P pools in eight soil samples that are representative of a wide type of soils. The performance of our SPD model was better for labile P, secondary mineral P, and occluded P than for nonoccluded organic P (Po) and primary mineral P. All parameters describing soil P dynamics were approximately constrained by the data sets. The average turnover rates were labile P 0.040 g g⁻¹day⁻¹, nonoccluded Po 0.051 g g⁻¹day⁻¹, secondary mineral P 0.023 g g⁻¹day⁻¹, primary mineral P 0.00088 g g⁻¹day⁻¹, occluded Po 0.0066 g g⁻¹day⁻¹, and occluded inorganic P 0.0065 g g⁻¹day⁻¹, in the greenhouse environment studied. Labile P was transferred on average more to nonoccluded Po (transfer coefficient of 0.42) and secondary mineral P (0.38) than to plants (0.20). Soil pH and organic C concentration were the key soil properties regulating the competition for P between plants and soil secondary minerals. The turnover rate of labile P was positively correlated with that of nonoccluded Po and secondary mineral P. The pool size of labile P was most sensitive to its turnover rate. Overall, we suggest data assimilation can contribute significantly to an improved understanding of soil P dynamics. 

   more » « less
5. CRISPR‐Cas9 Genome Editing in the Moss Physcomitrium (Formerly Physcomitrella ) patens

   https://doi.org/10.1002/cpz1.725  

   Wu, Shu‐Zon; Ryken, Samantha E.; Bezanilla, Magdalena (April 2023, Current Protocols)

   Abstract Until recently, precise genome editing has been limited to a few organisms. The ability of Cas9 to generate double stranded DNA breaks at specific genomic sites has greatly expanded molecular toolkits in many organisms and cell types. Before CRISPR‐Cas9 mediated genome editing,P. patenswas unique among plants in its ability to integrate DNA via homologous recombination. However, selection for homologous recombination events was required to obtain edited plants, limiting the types of editing that were possible. Now with CRISPR‐Cas9, molecular manipulations inP. patenshave greatly expanded. This protocol describes a method to generate a variety of different genome edits. The protocol describes a streamlined method to generate the Cas9/sgRNA expression constructs, design homology templates, transform, and quickly genotype plants. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Constructing the Cas9/sgRNA transient expression vector Alternate Protocol 1: Shortcut to generating single and pooled Cas9/sgRNA expression vectors Basic Protocol 2: Designing the oligonucleotide‐based homology‐directed repair (HDR) template Alternate Protocol 2: Designing the plasmid‐based HDR template Basic Protocol 3: Inducing genome editing by transforming CRISPR vector intoP. patensprotoplasts Basic Protocol 4: Identifying edited plants. 

   more » « less