Using Phylogenetic Analysis to Detect Market Substitution of Atlantic Salmon for Pacific Salmon: an Introductory Biology Laboratory Experiment

We describe a laboratory exercise developed for the cell and molecular biology quarter of a year-long majors\u27 undergraduate introductory biology sequence. In an analysis of salmon samples collected by students in their local stores and restaurants, DNA sequencing and phylogenetic analysis were used to detect market substitution of Atlantic salmon for Pacific salmon. This allowed students to apply molecular methods such as polymerase chain reaction (PCR) and DNA sequencing to a socially relevant issue

Goplana Dioscoreae-Alatae Nom. Nov and Other Uredinales On Dioscoreaceae: Nomenclature and Taxonomy

Among the sixteen species of rust fungi described on Dioscoreaceae, three require replacement names. This paper re-describes and proposes Goplana dioscoreae-alatae as a replacement name for Goplana dioscoreae Cummins, nom. illegit. We also propose Uredo dioscoreae-doryphorae as a replacement name for Uredo spinulosa Y. Ono, nom. illegit.; and Aecidium tumbayensis as a replacement name for Aecidium dioscoreae J.C. Lindq., nom. illegit. We discuss nomenclatural controversies surrounding these taxa

Marketplace Substitution of Atlantic Salmon for Pacific Salmon in Washington State Detected by DNA Barcoding

Accurate identification of seafood in the marketplace is an issue of international concern, due to high rates of market substitution of cheaper or more widely available species for expensive or high-demand species. Salmon samples from stores and restaurants throughout western Washington, USA were tested using DNA sequencing of a short section of the mitochondrial cytochrome c oxidase I (COI) gene (DNA barcoding) to identify Atlantic salmon substituted for Pacific salmon. Of 99 salmon samples, 11 (11%) were Atlantic salmon sold as Pacific salmon. More than 38% of restaurant samples were mislabeled to species, while only 7% of store samples were mislabeled. Market substitution rates were significantly greater in restaurants compared to stores, and consistently greater in winter compared to spring, although not significantly. The high market substitution rate in restaurants documents a pressing need for more monitoring and enforcement specifically in restaurants. DNA barcoding is a valuable tool for rapid and definitive authentication of salmon in the marketplace, and should be more widely adopted to discourage market substitution. (C) 2011 Elsevier Ltd. All rights reserved

Spatial Effects of Retention Trees on Mycorrhizas and Biomass of Douglas-Fir Seedlings

Retention forestry places seedlings in proximity to residual trees, exposing seedlings to additional sources of ectomycorrhizal fun-us (EMF) inoculum. To investigate this, Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings were planted near (2-6 m) and far (16-30 m) from 44- to 72-year-old residual Douglas-fir trees in western Washington, USA. From 1998 through 2000, seedling shoot and root biomass was assessed and EMF taxa were identified using morphology and sequence analysis of internal transcribed spacer and large subunit ribosomal RNA genes. Seedlings near residual trees had significantly greater ectomycorrhiza (ECM) abundance (percent active ECM root tips), less necrotic root tips, and higher root to shoot biomass ratios. Seedlings near trees had a richness index of 4.1 EMF taxa per seedling and 42 total taxa compared with 3.5 taxa per seedling and 33 total taxa for seedlings far from trees. Proximity to residual trees may increase seedling ECM abundance and diversity

Synopsis of Phytophthora with Accurate Scientific Names, Host Range, and Geographic Distribution

The genus Phytophthora includes species causing diseases such as late blight of potatoes, Phytophthora infestans, and sudden oak death and ramorum blight, P. ramorum. Because of the importance of diseases caused by Phytophthora, there is a need to have rapid access to the literature using their scientific names. The literature has been reviewed for all names in Phytophthora in order to provide the scientific name of each accepted species with authors and synonyms as well as the plant host range and worldwide geographic distribution. Within the genus Phytophthora, there are 87 accepted species and six infraspecific taxa. After compiling all available reports of Phytophthora, it was determined that 39 species and six infraspecific taxa, or about one-half of the accepted species, are not known to occur in the United States. The accurate scientific names of accepted species of Phytophthora are listed in two tables based on their presence or absence in the United States. Each species name is hyperlinked to databases that provide full synonymy and references documenting the host range and geographic distribution information. These data are continuously updated as new literature is published. Having rapid access to information about species of Phytophthora is critical for protecting the United States from the introduction of these potentially devastating pathogens

Metal Stress and Decreased Tree Growth in Response to Biosolids Application in Greenhouse Seedlings and In Situ Douglas-Fir Stands

To assess physiological impacts of biosolids on trees, metal contaminants and phytochelatins were measured in Douglas-fir stands amended with biosolids in 1982. A subsequent greenhouse study compared these same soils to soils amended with fresh wastewater treatment plant biosolids. Biosolids-amended field soils had significantly higher organic matter, lower pH, and elevated metals even after 25 years. In the field study, no beneficial growth effects were detected in biosolids-amended stands and in the greenhouse study both fresh and historic biosolids amendments resulted in lower seedling growth rates. Phytochelatins bioindicators of intracellular metal stress were elevated in foliage of biosolids-amended stands, and significantly higher in roots of seedlings grown with fresh biosolids. These results demonstrate that biosolids amendments have short- and long-term negative effects that may counteract the expected tree growth benefits. (C) 2011 Elsevier Ltd. All rights reserved

Effects of Synthetic Fertilizer on Coffee Yields and Ecosystem Services: Soil Glomalin and Parasitoids in a Costa Rican Coffee Agroecosystem

We explored the relationships between synthetic fertilizer use, yield, and ecosystem services in a coffee agroecosystem in the Tarrazú region in the central highlands of Costa Rica. Working in nine farms ranging from 0.3 to 2.7 ha in the CoopeTarrazú farmers\u27 cooperative, we focused on two important indicators of ecosystem services: biological control agents and mycorrhizal fungi. Biological control agents (especially parasitoid wasps) are essential for population regulation of herbivorous arthropods that reside in coffee agroecosystems. Mycorrhizal fungi contribute to plant nutrition and disease resistance and produce a highly stable protein, glomalin, which is critical for soil aggregation. Soil aggregates hedge against erosion, particularly in sloping soils, by improving porosity. Slopes in this study ranged from 4% to 66%. We manipulated synthetic fertilizer levels in experimental plots ranging from 6.9% increase to 53.3% decrease in total N relative to control plots that received a standard amount of fertilizer. The effects on coffee yields, soil glomalin production by mycorrhizal fungi, and wasp diversity were examined. Yield and glomalin decreased, but parasitoid diversity increased with greater reductions in fertilizer application six months after application. Reducing fertilizer use may bolster biological control assemblages, while glomalin is more directly dependent on plant production

Fourteen Recommendations to Create a More Inclusive Environment for LGBTQ+ Individuals in Academic Biology

Individuals who identify as lesbian, gay, bisexual, transgender, queer, and otherwise nonstraight and/or non-cisgender (LGBTQ+) have often not felt welcome or represented in the biology community. Additionally, biology can present unique challenges for LGBTQ+ students because of the relationship between certain biology topics and their LGBTQ+ identities. Currently, there is no centralized set of guidelines to make biology learning environments more inclusive for LGBTQ+ individuals. Rooted in prior literature and the collective expertise of the authors who identify as members and allies of the LGBTQ+ community, we present a set of actionable recommendations to help biologists, biology educators, and biology education researchers be more inclusive of individuals with LGBTQ+ identities. These recommendations are intended to increase awareness of LGBTQ+ identities and spark conversations about transforming biology learning spaces and the broader academic biology community to become more inclusive of LGBTQ+ individuals