When virulence originates from non-agricultural hosts: New insights into plant breeding

Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence – the allele that allows pathogens to overcome resistance – is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

<p>Abstract</p> <p>Background</p> <p>Microarrays are a popular tool used in experiments to measure gene expression levels. Improving the reproducibility of microarray results produced by different chips from various manufacturers is important to create comparable and combinable experimental results. Alternative splicing has been cited as a possible cause of differences in expression measurements across platforms, though no study to this point has been conducted to show its influence in cross-platform differences.</p> <p>Results</p> <p>Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity.</p> <p>Conclusion</p> <p>The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms.</p

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

BACKGROUND: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis. RESULTS: Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. CONCLUSION: We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software

The Las Vegas Monorail, an innovative solution for public transportation problems within the resort corridor

The Las Vegas Monorail project is the first and quite possibly the only private sector endeavor to construct mass transit grade transportation at no cost to the taxpayer, and with no public sector investment, subsidy, or guarantee. The Las Vegas Monorail project follows a structure similar to the innovative toll road projects of the last decade, illustrating how other transportation problems can be solved by similar procedures. This study provides an opportunity to get an inside look at the process of designing, building, operating, maintaining, and financing a major transportation project in Las Vegas and the unique cooperation between public and private entities

Simulating the Multi-Epoch Direct Detection Technique to Isolate the Thermal Emission of the Non-Transiting Hot Jupiter HD187123B

We report the 6.5$\sigma$ detection of water from the hot Jupiter HD187123b with a Keplerian orbital velocity $K_p$ of 53 $\pm$ 13 km/s. This high confidence detection is made using a multi-epoch, high resolution, cross correlation technique, and corresponds to a planetary mass of 1.4$^{+0.5}_{-0.3}$ $M_J$ and an orbital inclination of 21 $\pm$ 5$^{\circ}$. The technique works by treating the planet/star system as a spectroscopic binary and obtaining high signal-to-noise, high resolution observations at multiple points across the planet's orbit to constrain the system's binary dynamical motion. All together, seven epochs of Keck/NIRSPEC $L$-band observations were obtained, with five before the instrument upgrade and two after. Using high resolution SCARLET planetary and PHOENIX stellar spectral models, along with a line-by-line telluric absorption model, we were able to drastically increase the confidence of the detection by running simulations that could reproduce, and thus remove, the non-random structured noise in the final likelihood space well. The ability to predict multi-epoch results will be extremely useful for furthering the technique. Here, we use these simulations to compare three different approaches to combining the cross correlations of high resolution spectra and find that the Zucker 2003 log(L) approach is least affected by unwanted planet/star correlation for our HD187123 data set. Furthermore, we find that the same total S/N spread across an orbit in many, lower S/N epochs rather than fewer, higher S/N epochs could provide a more efficient detection. This work provides a necessary validation of multi-epoch simulations which can be used to guide future observations and will be key to studying the atmospheres of further separated, non-transiting exoplanets.Comment: Accepted to AJ, 14 pages, 10 figure

A qualitative examination of home and neighborhood environments for obesity prevention in rural adults

<p>Abstract</p> <p>Background</p> <p>The home and neighborhood environments may be important in obesity prevention by virtue of food availability, food preparation, cues and opportunities for physical activity, and family support. To date, little research has examined how home and neighborhood environments in rural communities may support or hinder healthy eating and physical activity. This paper reports characteristics of rural homes and neighborhoods related to physical activity environments, availability of healthy foods, and family support for physical activity and maintaining an ideal body weight.</p> <p>Methods</p> <p>In-depth interviews were conducted with 60 African American and White adults over 50 years of age in two rural counties in Southwest Georgia. Interviews were transcribed verbatim and coded independently by two members of the research team using standard methods of qualitative analysis. Themes were then identified and data matrices were used to identify patterns by gender or race.</p> <p>Results</p> <p>Neighborhood features that supported physical activity were plenty of land, minimal traffic and living in a safe and friendly neighborhood. The major barrier was lack of recreational facilities. The majority of participants were not physically active with their family members due to schedule conflicts and lack of time. Family member-initiated efforts to encourage physical activity met with mixed results, with refusals, procrastination, and increased activity all reported. Participants generally reported it was easy to get healthy foods, although cost barriers and the need to drive to a larger town for a supermarket with good variety were noted as obstacles. Family conversations about weight had occurred for about half of the participants, with reactions ranging from agreement about the need to lose weight to frustration.</p> <p>Conclusion</p> <p>This study suggests that successful environmental change strategies to promote physical activity and healthy eating in rural neighborhoods may differ from those used in urban neighborhoods. The findings also provide insight into the complexities of family support for physical activity and maintaining a healthy weight. Addressing socio-ecologic factors has the potential to increase healthy behaviors and decrease the prevalence of obesity among rural residents.</p