Manual for starch gel electrophoresis: A method for the detection of genetic variation

The procedure to conduct horizontal starch gel electrophoresis on enzymes is described in detail. Areas covered are (I) collection and storage of specimens, (2) preparation of tissues, (3) preparation of a starch gel, (4) application of enzyme extracts to a gel, (5) setting up a gel for electrophoresis, (6) slicing a gel, and (7) staining a gel. Recipes are also included for 47 enzyme stains and 3 selected gel buffers. (PDF file contains 26 pages.

Stock Composition of Some Sockeye Salmon, Oncorhynchus nerka, Catches in Southeast Alaska, Based on Incidence of Allozyme Variants, Freshwater Ages, and a Brain-Tissue Parasite

The incidence of four discrete characters of individual sockeye salmon -two genetically inherited proteins (PGM-1*and PGM-2*), freshwater age at migration, and the presence of the brain-tissue parasite Myxobolus arcticus-in weekly samples from two Alaskan fisheries (Noyes Island in 1986 and Sumner Strait in 1987) were used to infer stock composition of the catches based on corresponding character samples from 73 Alaskan and Canadian stocks. Estimated contributions of 13 stock groups, formed on the basis of character similarity of their members, were roughly consistent with expectations from tagging experiments, knowledge of stock magnitudes, and similar assessments from scales. Imprecision of the estimated contributions by the 13 stock groups limited their practical value; but variability was much reduced for combined estimated contributions by two inclusive categories, namely stock groups whose members had either high or low brainparasite prevalence. Noyes Island catches consisted predominantly of unparasitized fish, most of which were probably of Canadian origin. The majority of Sumner Strait catches consisted of parasitized fish, whose freshwater origins may have been in Alaska or Canada. (PDF file contains 27 pages.

A herança musical da escravidão

A escravidão colocou em contato povos de diferentes origens em situações radicalmente novas, em um contexto de violência e dominação extremas. Apesar disso, tais contatos, a despeito da brutalidade que os fundava e das profundas desigualdades então engendradas, resultaram também em processos de mistura e criação cultural que produziram, especialmente, novas formas de expressão musicais. Este artigo busca analisar, de uma perspectiva comparada, processos sociais de criação musical no contexto de sociedades escravagistas ou pós-escravagistas, especialmente o surgimento de novas formas musicas nos Estados Unidos e na África do Sul

Population Genetic Structure and Life History Variability in \u3ci\u3eOncorhynchus nerka\u3c/i\u3e from the Snake River Basin

We used the variation at 64 allozyme loci to examine genetic relationships among 32 samples of sockeye salmon Oncorhynchus nerka and kokanee (resident sockeye salmon) from the Snake River basin and other North American locations. The genetic differentiation among populations was pronounced: Wright’s FST was higher (0.244) than has been reported in any other study of Pacific salmon. A detailed examination of the O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve the relationships between the resident and anadromous forms. In Redfish Lake, adult sockeye salmon that returned in 1991–1993 were genetically distinct from local kokanee but similar to a small group of “residual” sockeye salmon discovered in the lake in 1992. This result is consistent with the hypothesis that the original sockeye salmon population was not extirpated by Sunbeam Dam early in this century. Populations of O. nerka that appear to be native to the Snake River were also found in Alturas Lake, Stanley Lake, and Warm Lake, although the latter two lakes also showed evidence of nonnative gene pools. Kokanee sampled from Pettit Lake are clearly the result of an introduction of late-spawning kokanee from northern Idaho, and we found evidence of two O. nerka gene pools in Wallowa Lake, both traceable to introductions of nonnative kokanee

A Genetic Survey of English Sole Populations in the Salish Sea

This summer I interned at the Northwest Fisheries Science Center in Seattle, WA and participated in NOAA’s Salish Sea Project. The Salish Sea Project’s goal is to identify genetically distinctive groups of species in the Salish Sea that may have unique evolutionary and/or adaptive backgrounds. These findings will allow NOAA to promote and monitor the natural production of species in the Salish Sea, to select representative populations for experimental work regarding pollution, ocean acidification and climate change, to contribute to managing the ecosystem for intra- and inter-species diversity, and to help make informed decisions about adaptive management and marine protected areas (MPA). Our focus for the summer was English Sole (Parophrys vetulus). We performed microsatellite analysis on 480 individuals over ten populations and used factoid correspondence analysis to summarize the variation across five loci. Significant differences were seen among only three of the ten populations. These results are preliminary; up to fifteen loci should be analyzed before a conclusion is reached on the genetic variability of these populations. We would also like to include English Sole populations north of the Strait of Georgia, and along the Oregon coast

Assembling a multi species view of population level differentiation of marine life in the Salish Sea.

Our goal is to understand the Salish Sea ecosystem more completely by studying the population genetics of multiple species, plants and animals, covering a variety of habitats, trophic, and taxonomic groups. We believe these data will help inform ecosystem based management, e.g., the practical design of a network of marine protected areas or reservoirs (MPA). We present results of a population genetic study of English sole collected within the Salish Sea and from offshore as far north as Haida Gwaii, a study done in cooperation with NOAA Teacher in the Laboratory, Canadian Department of Fisheries and Oceans (CDFO), and Washington Department of Fish and Wildlife (WDFW). We also illustrate a sample design and the cooperative nature of this type of work by presenting the status of a new genetic and phenetic study of spot prawn that has been initiated with funds from The Suquamish Tribe and in cooperation with CDFO; WDFW; The Lummi, Muckleshoot, Nisqually, and Swinomish tribes; Vancouver Aquarium; and Mariner High School, Everett, WA. Patterns of population variability demonstrated from work in other research laboratories for Olympia oysters, Pacific herring and hake, and yellow eye rockfish are discussed. The ecosystem is experiencing change, including climate change, ocean acidification, and urban growth, and identifying the geographic nature of population variability for a variety of species will help us establish better tools for monitoring and protecting species, species groups, and habitats. In the process, we will learn what abiotic and biotic factors affect the patterns genetic connectivity for different marine taxonomic groups, and therefore be in a better position to understand, model, and track population responses to environmental change. Collaborative and cooperative work like this highlights the diversity of animal and plant life that is found but rarely recognized in our marine backyards

Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas

<div><p>Avian leukosis virus (ALV) is a simple retrovirus that causes a wide range of tumors in chickens, the most common of which are B-cell lymphomas. The viral genome integrates into the host genome and uses its strong promoter and enhancer sequences to alter the expression of nearby genes, frequently inducing tumors. In this study, we compare the preferences for ALV integration sites in cultured cells and in tumors, by analysis of over 87,000 unique integration sites. In tissue culture we observed integration was relatively random with slight preferences for genes, transcription start sites and CpG islands. We also observed a preference for integrations in or near expressed and spliced genes. The integration pattern in cultured cells changed over the course of selection for oncogenic characteristics in tumors. In comparison to tissue culture, ALV integrations are more highly selected for proximity to transcription start sites in tumors. There is also a significant selection of ALV integrations away from CpG islands in the highly clonally expanded cells in tumors. Additionally, we utilized a high throughput method to quantify the magnitude of clonality in different stages of tumorigenesis. An ALV-induced tumor carries between 700 and 3000 unique integrations, with an average of 2.3 to 4 copies of proviral DNA per infected cell. We observed increasing tumor clonality during progression of B-cell lymphomas and identified gene players (especially <i>TERT</i> and <i>MYB</i>) and biological processes involved in tumor progression.</p></div

Genetic Characterization of <i>Oncorhynchus mykiss</i> Prior to Dam Removal with Implications for Recolonization of the Elwha River Watershed, Washington

<p>For more than 100 years, two dams blocked upstream migration of steelhead <i>Oncorhynchus mykiss</i> (anadromous Rainbow Trout) on the Elwha River, Washington. Prior to the removal of both dams (completed in 2015), 30 spatiotemporal collections of resident Rainbow Trout, steelhead, hatchery steelhead, and hatchery-derived Rainbow Trout (1,949 individuals) were made from 17 sites in the river, and the pattern of genetic diversity and connectivity were evaluated using 13 microsatellite loci. Wild-origin steelhead spawned below the downstream dam and were genetically distinguishable from upriver (above dam) resident Rainbow Trout (<i>F</i>_ST = 0.034), and the resident Rainbow Trout segregated into two distinct groups (<i>F</i>_ST = 0.056). Nonnative-origin hatchery steelhead varied from the indigenous steelhead (<i>F</i>_ST = 0.029), and the hatchery trout differed from the resident trout (<i>F</i>_ST = 0.163). Collections of resident Rainbow Trout from the upper portion of the basin were distinguished by lower estimates of genetic variability (<i>H_e, A</i>_R, and A/L) and effective population size compared with resident Rainbow Trout in the middle reaches of the Elwha River. The break between the two trout groups coincided with Rica Canyon, 8 river kilometers upstream from the Glines Canyon Dam (the upstream dam), suggesting that the upper and middle trout groups represent historic <i>O. mykiss</i> groups separated by flow conditions in the canyon prior to dam construction. Anticipating the potential for genetic exchange between steelhead and resident Rainbow Trout following dam removal, we evaluated the ability of the microsatellite baseline to distinguish F₁ crosses between the life history groups with computer simulations. These results demonstrate how a genetic baseline can be used as a conservation management tool to measure potential genetic introgression among resident populations and recolonizing anadromous populations.</p> <p>Received June 17, 2016; accepted October 10, 2016 Published online December 12, 2016 </p

Functional classifications overrepresented among the clonally expanded integrations.

<p>Five functional categories that are significantly overrepresented among the neoplastic follicles, primary tumors and metastases, are illustrated as a bar graph. The horizontal bars represent statistical significance as defined by −log (p-values). The integrations are analyzed by g:profiler software using a random list of integrations (n = 5000) as background. Since there are no overrepresented pathways involving the integration sites in inflammation or non-tumor samples, the bars are not visible. Due to use of varying sample size, all the analysis was adjusted for multiple testing with unequal sample size using the Mann Whitney U test.</p