In Vivo validation of a bioinformatics based tool to identify reduced replication capacity in HIV-1.

Although antiretroviral drug resistance is common in treated HIV infected individuals, it is not a consistent indicator of HIV morbidity and mortality. To the contrary, HIV resistance-associated mutations may lead to changes in viral fitness that are beneficial to infected individuals. Using a bioinformatics-based model to assess the effects of numerous drug resistance mutations, we determined that the D30N mutation in HIV-1 protease had the largest decrease in replication capacity among known protease resistance mutations. To test this in silico result in an in vivo environment, we constructed several drug-resistant mutant HIV-1 strains and compared their relative fitness utilizing the SCID-hu mouse model. We found HIV-1 containing the D30N mutation had a significant defect in vivo, showing impaired replication kinetics and a decreased ability to deplete CD4+ thymocytes, compared to the wild-type or virus without the D30N mutation. In comparison, virus containing the M184V mutation in reverse transcriptase, which shows decreased replication capacity in vitro, did not have an effect on viral fitness in vivo. Thus, in this study we have verified an in silico bioinformatics result with a biological assessment to identify a unique mutation in HIV-1 that has a significant fitness defect in vivo

The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations

Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (Pcd), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when Pcd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors

A qualitative study of the views of residents with dementia, their relatives and staff about work practice in long-term care settings

Background: Most people living in 24-hour care settings have dementia, and little is known about what makes long-term care a positive experience for them.Method: This carer-led qualitative study examined working practices in 24-hour long-term care-settings, including hospitals, nursing and residential homes, with the aim of finding out and making recommendations about such settings. Using semi-structured interviews, managers, nurses and care assistants were asked about work practices, such as how they coped with difficult behavior, about shifts, staffing levels, staff retention and training. Relatives of residents with dementia were asked about their role and perceptions of the care provided, and residents were asked for their opinions of their care.Results: Staff reported that residents presented with increasingly challenging behavior compared to the past, and that sometimes staffing levels and skills were inadequate. Of all the settings, hospitals had the most problems with staffing levels and retention, staff-relative relationships and staff support systems. Relatives saw their own role as positive. People with dementia of varying severity could usefully evaluate some of the services they received.Discussion: Dementia-specific training and education of staff in all long-term care-settings, including induction, should address the management of problem behavior in dementia and thereby improve staff fulfilment and relatives' satisfaction. The long-stay hospital may not be appropriate as a "home for life" for those with dementia, and we recommend that long-stay care settings should be able to cater flexibly for a range of resident needs

Postcard: D3321. Lyle St., West Mineral, Kansas

This black and white photographic postcard features a view of a street in West Mineral, Kansas. Buildings line the left and right side. A muddy dirt road runs the length of the street. Printed text is at the bottom left of the card. Handwriting is on the back of the card.https://scholars.fhsu.edu/tj_postcards/1601/thumbnail.jp

MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base

Surprisingly low limits of selection in plant domestication

Current debate concerns the pace at which domesticated plants emerged from cultivated wild populations and how many genes were involved. Using an individual-based model, based on the assumptions of Haldane and Maynard Smith, respectively, we estimate that a surprisingly low number of 50–100 loci are the most that could be under selection in a cultivation regime at the selection strengths observed in the archaeological record. This finding is robust to attempts to rescue populations from extinction through selection from high standing genetic variation, gene flow, and the Maynard Smith-based model of threshold selection. Selective sweeps come at a cost, reducing the capacity of plants to adapt to new environments, which may contribute to the explanation of why selective sweeps have not been detected more frequently and why expansion of the agrarian package during the Neolithic was so frequently associated with collapse

A performance evaluation of commercial fibrinogen reference preparations and assays for Clauss and PT-derived fibrinogen

The wide availability of fibrinogen estimations based on the prothrombin time (PT-Fg) has caused concern about the variability and clinical utility of fibrinogen assays. In a multi-centre study, we investigated fibrinogen assays using various reagents and analysers, Clauss assays generally gave good agreement, although one reagent gave 15-30% higher values in DIC and thrombolysis. Two commercial reference preparations had much lower potencies than the manufacturers declared, and plasma turbidity influenced parallelism in some Clauss assays, PT-Fg assays gave higher values than Clauss and showed calibrant dependent effects, the degree of disparity correlating with calibrant and test sample turbidity. Analyser and thromboplastin dependent differences were noted. The relationship between Clauss and PT-Fg assays was sigmoid, and the plateau of maximal PT-Fg differed by about 2 g/l between reagents. ELISA and immunonephelometric assays correlated well, but with a high degree of scatter. Antigen levels were higher than Clauss, but slightly lower than PT-Fg assays, which appeared to be influenced by degraded fibrinogen. Clauss assays are generally reproducible between centres, analysers and reagents, but PT-Fg assays are not reliable in clinical settings

Multiple Scale Den Site Selection by Swift Foxes, Vulpes velox, in Southeastern Colorado

Predation by Coyotes (Canis latrans) is a major source of mortality in Swift Fox (Vulpes velox) populations. Year-round den use by Swift Foxes is likely to be a predator avoidance strategy. Due to the importance of denning to Swift Fox ecology, we recorded den site selection of Swift Foxes in southeastern Colorado. Den site selection was recorded at two scales: microhabitat characteristics at the den and den placement within the home range. The number of den entrances, height and width of each entrance, aspect, hill position, slope, percent rock in soil, vegetative cover, and horizontal foliar density of 42 Swift Fox dens were examined during December 1999 – April 2000. This was compared to the same microhabitat characteristics at 42 random sites within Swift Fox home ranges to determine if Swift Foxes were using site characteristics according to their availability. Our results indicated that Swift Foxes were not highly selective of den sites based on the microhabitat characteristics evaluated in this study, although Swift Foxes selected areas of intermediate rock percentages. In addition, Swift Foxes were radio-tracked throughout the sample period and the location and frequency of use of known dens were recorded. Within the core area of home ranges, Swift Foxes used more dens (mean = 3.51 ± 1.70 (SD)), and had a higher frequency of use of dens (mean = 8.20 ± 6.01) than in the mid-range area (number of dens, mean = 0.90 ± 0.94; frequency, mean = 1.27 ± 2.12) and the boundary area (number of dens, mean = 0.34 ± 0.53; frequency, mean = 0.45 ± 0.93) of the home range. We discuss our results in terms of the importance of dens in facilitating escape from Coyotes. These results illustrate the need for examining den site selection at multiple scales to determine all selection factors, and to provide information useful for recovery and management efforts for this species