Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression

Heritable differences in transcribed RNA levels can be mapped as quantitative trait loci (QTLs). Transcribed RNA levels are often measured by hybridization to microarrays of oligonucleotide probes, in which each transcript is represented by multiple probes. The use of recombinant inbred lines allows an estimate of the heritability of expression measured by individual probes. This heritability varies greatly. We have tested heritability-weighted averages to define expression of a transcript and found that these allow detection of more QTLs than previously described methods

Clustering Hyperspectral Imagery for Improved Adaptive Matched Filter Performance

This paper offers improvements to adaptive matched filter (AMF) performance by addressing correlation and non-homogeneity problems inherent to hyperspectral imagery (HSI). The estimation of the mean vector and covariance matrix of the background should be calculated using “target-free” data. This statement reflects the difficulty that including target data in estimates of the mean vector and covariance matrix of the background could entail. This data could act as statistical outliers and severely contaminate the estimators. This fact serves as the impetus for a 2-stage process: First, attempt to remove the target data from the background by way of the employment of anomaly detectors. Next, with remaining data being relatively “target-free” the way is cleared for signature matching. Relative to the first stage, we were able to test seven different anomaly detectors, some of which are designed specifically to deal with the spatial correlation of HSI data and/or the presence of anomalous pixels in local or global mean and covariance estimators. Relative to the second stage, we investigated the use of cluster analytic methods to boost AMF performance. The research shows that accounting for spatial correlation effects in the detector yields nearly “target-free” data for use in an AMF that is greatly benefitted through the use of cluster analysis methods

Comparison of Orchid Bee (Hymenoptera: Apidae) Species Composition Collected with Four Chemical Attractants

Orchid bees (Hymenoptera: Apidae: Euglossini) are a diverse and important group of Neotropical pollinators. Numerous chemicals have been used in sampling orchid bees, and species-specific attraction, particularly of males, to these chemicals is well known. However, there have been few studies that have quantified differences in the species composition of orchid bees attracted to particular chemicals. In this study, we compared the abundance and species composition of orchid bees collected with 4 commonly used attractants: benzyl acetate, eucalyptol (or cineole), eugenol, and methyl salicylate. Eucalyptol collected the greatest abundance and species richness of orchid bees. Indicator species analysis revealed that 3 species, Euglossa imperialis Cockerell, Euglossa obtusa Dressler, and Eufriesea mexicana (Mocsáry), were significantly associated with eucalyptol, and 1, Eulaema marcii Nemésio, with benzyl acetate. The multi-response permutation procedure revealed relatively large differences in species composition of orchid bees collected with eucalyptol vs. benzyl acetate and eucalyptol vs. eugenol. Our results showed that eucalyptol and benzyl acetate were the most effective and complimentary attractants, but even less effective attractants such as eugenol may attract novel species

Vegetative Community Development over 30 Years within Mixed Pine-Hardwood Mine Reclamation sites in east Texas

The practice of mine reclamation aims to balance the energy needs of society with proactive environmental restoration of degraded land, and long-term studies of vegetative community development on reclaimed mine land have been invaluable in developing effective reclamation practices. This study investigated vegetative community characteristics (composition, richness, species importance)over a 30 year time frame in planted mixed pine-hardwood areas on reclaimed surface coal mine land in East Texas,United States. Reclaimed sites werecompared vegetatively to unmined reference forests. A chronological pattern wasshown for reclaimedcommunity developmentin both understory and overstorystrata. Understory community development exhibitednatural patterns, while theoverstory community varied with different groups of planted species. The olderreclaimed sites were most similar to unmined reference sites. Dissimilaritiesbetween mined and unmined communities were also apparent; for example, thewoody vine community of reference sites was much more substantial in midstoryand overstory strata as compared to reclaimed sites. Overall, this study providedbaseline ecological information about these plant communities that may assistland managers and researchers in furthering their development of reclamation techniques and attainment of reclamation goals

Raman Spectroscopy of Synthetic Antimicrobial Frog Peptides Magainin 2a and PGLa

Magainin and PGLa are 23- and 21-residue peptides isolated from the skin of the African clawed frog Xenopus lueuis. They protect the frog from infection and exhibit a broad-spectrum antimicrobial activity in vitro. The mechanism of this activity involves the interaction of magainin with microbial membranes. We have measured the secondary structure and membrane-perturbing ability of these peptides to obtain information about this mechanism. Our results show that mgn2a forms a helix with an average length of less than 20 Å upon binding to liposomes. At high concentrations (50 mg/mL) mgn2a spontaneously solubilizes phosphatidylcholine liposomes at temperatures above the gel-liquid-crystalline phase transition. Mgn2a appears to bind to the surface of liposomes made of negatively charged lipids without spontaneously penetrating the bilayer. Finally, mgn2a and PGLa interact together with liposomes in a synergistic way that enhances the helix content of one or both of the peptides and allows the peptides to more easily penetrate the bilayer. PGLa mixed with a small nonperturbing amount of magainin 2 amide is 25-43 times as potent as PGLa alone at inducing the release of carboxyfluorescein from liposomes. The results suggest that the mechanism of antimicrobial activity does not involve a channel formed by transmembrane helical peptides

Rating the Financial Health of U.S. Production Agriculture using Synthetic Credit Rating

Agribusiness, Agricultural and Food Policy, Production Economics,