Identifying safety strategies for on-farm grain bins using risk analysis

The potential for grain bin accidents exists each year on Arkansas farms and farms across the nation. The trend toward increasing utilization of on-farm grain drying and storage could lead to an increase in grain bin accidents. The sharp contrast between a safe, efficient operation and one that leads to injury or death can be represented as sets of farmer-decisions and subsequent chance events. A model was constructed to define the risk associated with grain bin entry and inbin activity so that safety interventions could be identified and implemented to reduce the probability of injury and death. A survey was distributed to Arkansas grain farmers to gather data on the level of safety education, storage techniques, operations management, and other parameters. The data collected from the survey provided quantitative input of many of the model’s probability-distribution functions. Using a fault tree (with parallel modes of failure) in conjunction with a Monte Carlo simulation technique, we evaluated six safety intervention strategies and identified the one with the greatest potential for reducing the risk of serous injury or death. As part of senior design in biological engineering, plans are underway to design and test a probe that can locate and break bridged grain (a common risk factor in grain bin management) while working outside the bin on the ground

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns

Estimating the sequence complexity of a random oligonucleotide population by using in vitro thermal melting and Cot analyses

Randomly generated oligonucleotide populations have a high potential to serve as pools for selecting non-cross-hybridizing sequences, which are useful for nanoscale self-assembly and biological and biomedical applications, as well as for DNA computing applications. In this study a nonlinear kinetic model was developed for the complexity estimation of large unknown polynucleotide populations and was experimentally verified. The model was implemented to estimate the sequence complexity of the random 20 base-pair population after in vitro renaturation experiments. The kinetic behaviors of the random 20mers were also evaluated with in vitro thermal melting experiments. This study represents a step in realizing the potential of random oligonucleotides for DNA computing and nanoscale self-assembly applications for biology and medicine. © 2005 Elsevier Inc. All rights reserved

Functional and Biological Determinants Affecting the Duration of Action and Efficacy of Anti-(+)-Methamphetamine Monoclonal Antibodies in Rats

These studies examined the in vivo pharmacokinetics and efficacy of five anti-methamphetamine monoclonal antibodies (mAbs, KD values from 11 to 250 nM) in rats. While no substantive differences in mAb systemic clearance (t1/2 = 6.1-6.9 days) were found, in vivo function was significantly reduced within 1-3 days for four of the five mAbs. Only mAb4G9 was capable of prolonged efficacy, as judged by prolonged high methamphetamine serum concentrations. MAb4G9 also maintained high amphetamine serum concentrations, along with reductions in methamphetamine and amphetamine brain concentrations, indicating neuroprotection. The combination of broad specificity for methamphetamine-like drugs, high affinity, and prolonged action in vivo suggests mAb4G9 is a potentially efficacious medication for treating human methamphetamine-related medical diseases

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns