Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.Keywords: conservation genetics, ecological genetics, captive populations, conservation biology, life history evolution, hybridization, population genetics, fisheries managemen

A hybrid approach to protein folding problem integrating constraint programming with local search

<p>Abstract</p> <p>Background</p> <p>The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search.</p> <p>Results</p> <p>Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach.</p> <p>Conclusion</p> <p>Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.</p

Comprehensive determination of 3JHNHα for unfolded proteins using 13C′-resolved spin-echo difference spectroscopy

An experiment is presented to determine 3JHNHα coupling constants, with significant advantages for applications to unfolded proteins. The determination of coupling constants for the peptide chain using 1D 1H, or 2D and 3D 1H-15N correlation spectroscopy is often hampered by extensive resonance overlap when dealing with flexible, disordered proteins. In the experiment detailed here, the overlap problem is largely circumvented by recording 1H-13C′ correlation spectra, which demonstrate superior resolution for unfolded proteins. J-coupling constants are extracted from the peak intensities in a pair of 2D spin-echo difference experiments, affording rapid acquisition of the coupling data. In an application to the cytoplasmic domain of human neuroligin-3 (hNlg3cyt) data were obtained for 78 residues, compared to 54 coupling constants obtained from a 3D HNHA experiment. The coupling constants suggest that hNlg3cyt is intrinsically disordered, with little propensity for structure

Work-Family Domain Interference By Technology Use During Nonwork Times: An Investigation Of Cyberstress, Work-Family Conflict, And Boundary Management

The purpose of the current study is to investigate the role that technological interruption has on non-work time (i.e., hours at home during the evenings and weekend for daytime shift workers). Specifically, the study investigates experienced stress due to actual work interruptions (e.g., urgent emails, texts, or calls related to work) and a perceived ‘tether’ to work (e.g., a self-imposed pressure or perceived need to check email during time at home) and their relationship with work-family conflict and boundary management preferences. The study found some interesting evidence that stress due to technology can be a problem in the work-family domain and that cyberstress is a unique construct. Although the current study experienced limitations, it does provide a framework for future studies to continue to investigate stress due to technology use in the work-family domain.in

Photocycle of Photoactive Yellow Protein

The purpose of the present study was to determine if reasons reported for not having enough food, food resource management behaviors, nutrient intakes, and diet quality of Community Nutrition Education Program (CNEP) participants differed by food security status. This was a descriptive study consisting of 366 female participants. Food security status was assessed using the United States Department of Agricultures (USDA) 6-item food security measure. Nutrient intake was assessed using a 24-hour food recall. Diet Quality was assessed using the USDA Healthy Eating Index (HEI). Food resource management behaviors were assessed using the CNEP survey. A significantly greater percentage of food insecure and food insecure with hunger participants reported not having enough money for food (p&amp;#8804;.05). More than half of the participants who reported that it was too hard to get to the store were food insecure or food insecure with hunger (p&amp;#8804;.05). Over 75% of participants who reported that they were not able to prepare food because of a health problem were food insecure and food insecure with hunger (p&amp;#8804;.05). Almost all of the participants who reported that they had no way to cook their food were food insecure and food insecure with hunger (p&amp;#8804;.05). As food security status worsened more participants participated in gleaning (p&amp;#8804;.05). Estimated nutrient intakes were not significantly different across food security status. There were no significant differences between food security status and diet quality. In a low-income sample of CNEP participants, several reasons for not having enough food and the food resource management behavior of gleaning were significant by food security status. Nutrient intake and diet quality was not associated with food security status.Department of Nutritional Science

Age-Related Shifts in Housing and Transportation Demand : A Multidisciplinary Study Conducted for Metro by Portland State University\u27s College of Urban and Public Affairs, Final Report

Understanding where middle-aged and older adults live, where they are moving, how they get around, and the factors influencing these decisions is essential for planning for the future. To gain an understanding of the impact of age-related shifts on housing and transportation demand, Portland State University\u27s College of Urban and Public Affairs, via its Institute on Aging, was contracted to conduct a review of the literature and to analyze existing key local and national data sources. A multidisciplinary team of faculty and graduate students was assembled and performed the work in the summer of 2006. The literature reviewed and the analyses presented here are intended to inform Metro\u27s Regional Forecast and modeling assumptions and to stimulate policy discussions pertaining to managing the region\u27s land supply and investing in transportation infrastructure

Data from: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive vs. neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring run offspring that returned in spring (spring run), and fall run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally-listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11 and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing

DPJ_ FRH09 9Msats and 7 genes (07 19 12)rev

Excel file containing genotype data for Feather River Chinook salmon. Individuals are identified by population in each row: Fall, Spring and FRS (fall return spring). Loci are designated by column with the nine microsatellite listed followed by seven adaptive markers