Nanomaterials for Double-Stranded RNA Delivery

RNA interference has enormous potential as a potent, specific, and environmentally friendly alternative to small molecule pesticides for crop protection. The use of exogenous double-stranded RNA offers flexibility in targeting and use in crops in which transgenic manipulation is not an option. The combination of RNAi with nanotechnology offers further advantages that are not available with dsRNA alone. In this work, I have evaluated several different combinations of nanomaterials and polymers for use in RNAi-based pest control systems. First, I have characterized the use of chitosan/dsRNA polyplex nanoparticles for gene knockdown using the model nematode Caenorhabditis elegans. Though chitosan/dsRNA polyplexes are equally as effective as naked dsRNA for gene knockdown on a concentration basis, these materials are assimilated into cells in a manner independent of dsRNA specific transport proteins. The mechanism of uptake is likely clathrin-mediated endocytosis. In addition, I identify a significant and yet unreported side-effect associated with chitosan exposure, the dysregulation of a major myosin isoform. Next, I have determined the efficacy of chitosan/dsRNA polyplex nanoparticles under different environmental conditions. The presence of inorganic ions (phosphate and nitrate) at realistic environmental concentrations does not alter the efficacy of the nanoparticles for gene knockdown, nor do they inhibit knockdown by naked dsRNA. These conditions did not cause any significant changes to the hydrodynamic diameter or zeta potential of the particles themselves between treatments. By contrast, a pH higher than six and the presence of natural organic matter significantly reduce the efficacy of the nanomaterials at gene knockdown but leave knockdown by naked dsRNA unaffected. Though some changes in polyplex size are observed in the pH treatments, these changes are comparatively small, and particles remain well within the size that can be ingested by C. elegans. At pH 8, the charge of the particles is effectively neutral. Similarly, concentrations of natural organic matter \u3e2.5 mg/L cause a charge reversal of the particles, from strongly cationic to strongly anionic. Large aggregates are also visible in each of these treatments. Lastly, I characterize the efficacy of a suite of different polymer and solid core nanomaterials for dsRNA delivery, similar to the above. Poly-L-lysine, poly-L-arginine, Ge-doped imogolite, and poly-L-arginine-citrate coated Au nanoparticles all fail to cause any appreciable knockdown in the same C. elegans reporter system. Uptake of the polymers was exceedingly poor, and though the Au particles appear to have been ingested, there is no evidence of significant gene knockdown. Furthermore, poly-L-arginine caused significant injury to the mouthparts of C. elegans exposed to these materials. Layered double-hydroxide nanoparticles were successful at gene knockdown, and appear to function slightly better than naked dsRNA alone, and were translocated in C. elegans in a similar fashion to naked dsRNA. Taken together, these findings aid in the development of safe and effective RNAi biological control agents

Pion-proton scattering and isospin breaking in the Δ0−Δ++\Delta^0-\Delta^{++} system

We determine the mass and width of the $\Delta^{++}\ (\Delta^0)$ resonance from data on $\pi^+ p\ (\pi^- p)$ scattering both, in the pole of the $S$-matrix and conventional Breit-Wigner approaches to the scattering amplitude. We provide a simple formula that relates the two definitions for the parameters of the $\Delta$. Isospin symmetry breaking in the \d0-\dm system depends on the definition of the resonant properties: we find $M_0-M_{++} = 0.40 \pm 0.57\ {\rm MeV},\ \Gamma_0 -\Gamma_{++} = 6.89 \pm 0.95\ {\rm MeV}$ in the pole approach while $\wt{M}_0-\wt{M}_{++} = 2.25 \pm 0.68\ {\rm MeV},\ \wt{\Gamma}_0 - \wt{\Gamma}_{++} = 8.45 \pm 1.11\ {\rm MeV}$ in the conventional approach.Comment: Latex, 23 pages, two figures upon reques

Relaxed plasma equilibria and entropy-related plasma self-organization principles

The concept of plasma relaxation as a constrained energy minimization is reviewed. Recent work by the authors on generalizing this approach to partially relaxed three-dimensional plasma systems in a way consistent with chaos theory is discussed, with a view to clarifying the thermodynamic aspects of the variational approach used. Other entropy-related approaches to finding long-time steady states of turbulent or chaotic plasma systems are also briefly reviewed.Comment: Contribution to the Proceedings of the AMSI/MASCOS Concepts of Entropy and their Applications Workshop, Melbourne, Australia, November-December 2007, to be published in Entropy e-journal http://www.mdpi.org/entropy

Expanding CWD Disease Surveillance Options Using Environmental Contamination at Deer Signposts

1. Environmental surveillance can allow early detection of diseases, which increases management options and can improve disease trajectories. Chronic wasting disease (CWD) in cervids is a significant prion disease that has been spreading across North America since the 1960s, leading to cervid population declines and concern from hunters and state wildlife agencies. White-tailed deer have a unique breeding season behavior called scraping, where they deposit urine and saliva at shared sites. Since both these fluids can contain CWD prions, scrape sites have the potential to serve as sentinel sites for environmental surveillance of CWD.2. To examine this potential, we used camera traps to monitor deer behavior and collected environmental samples from 105 scrape sites. The 48 km2 study site was located at the center of the CWD zone in southwestern Tennessee (United States), where CWD prevalence is ~50%. We also sampled scrapes in northern Mississippi at the leading edge of the same CWD distribution to test the potential for early CWD detection using scrape sampling.3. From camera data, we identified 218 unique bucks visiting 105 scrapes, with a mean of 12.2 ± 7.5 bucks per scrape (mean ± SD, range 1–39) and individual bucks visiting a mean of 5.9 ± 4.6 monitored scrapes each (range 1–23).4. Using real-time quaking-induced conversion (RT-QuIC), we detected prion seeding activity in 20% of the soil and 41% of the licking branches of the scrape sites within the CWD study area, and in 25% of the soil and 11% of the licking branches of scrape sites sampled at the edge of the known CWD distribution.5. Our data show there is environmental prion contamination at scrape sites. This supports the idea that scrapes could serve as early warning sentinel sites for CWD surveillance through testing soil and licking branches for prion seeding ac-tivity, especially in areas with limited access to harvested deer samples

Robust rank aggregation for gene list integration and meta-analysis

Motivation: The continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously. To get the best out of all these alternatives, we need to integrate their results in an unbiased manner. Prioritized gene lists are a common result presentation method in genomic data analysis applications. Thus, the rank aggregation methods can become a useful and general solution for the integration task

Toxicogenomic responses of Caenorhabditis elegans to pristine and transformed zinc oxide nanoparticles

Manufactured nanoparticles (MNPs) undergo transformation immediately after they enter wastewater treatment streams and during their partitioning to sewage sludge, which is applied to agricultural soils in form of biosolids. We examined toxicogenomic responses of the model nematode Caenorhabditis elegans to pristine and transformed ZnO-MNPs (phosphatized pZnO- and sulfidized sZnO-MNPs). To account for the toxicity due to dissolved Zn, a ZnSO4 treatment was included. Transformation of ZnO-MNPs reduced their toxicity by nearly ten-fold, while there was almost no difference in the toxicity of pristine ZnO-MNPs and ZnSO4. This combined with the fact that far more dissolved Zn was released from ZnO- compared to pZnO- or sZnO-MNPs, suggests that dissolution of pristine ZnO-MNPs is one of the main drivers of their toxicity. Transcriptomic responses at the EC30 for reproduction resulted in a total of 1161 differentially expressed genes. Fifty percent of the genes differentially expressed in the ZnSO4 treatment, including the three metal responsive genes (mtl-1, mtl-2 and numr-1), were shared among all treatments, suggesting that responses to all forms of Zn could be partially attributed to dissolved Zn. However, the toxicity and transcriptomic responses in all MNP treatments cannot be fully explained by dissolved Zn. Two of the biological pathways identified, one essential for protein biosynthesis (Aminoacyl-tRNA biosynthesis) and another associated with detoxification (ABC transporters), were shared among pristine and one or both transformed ZnO-MNPs, but not ZnSO4. When comparing pristine and transformed ZnO-MNPs, 66% and 40% of genes were shared between ZnO-MNPs and sZnO-MNPs or pZnO-MNPs, respectively. This suggests greater similarity in transcriptomic responses between ZnO-MNPs and sZnO-MNPs, while toxicity mechanisms are more distinct for pZnO-MNPs, where 13 unique biological pathways were identified. Based on these pathways, the toxicity of pZnO-MNPs is likely to be associated with their adverse effect on digestion and metabolism

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Biological Process Linkage Networks

BACKGROUND. The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN). RESULTS. We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods. CONCLUSIONS. Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.Lynn and William Frankel Center for Computer Science; the Paul Ivanier center for robotics research and production; National Science Foundation (ITR-048715); National Human Genome Research Institute (1R33HG002850-01A1, R01 HG003367-01A1); National Institute of Health (U54 LM008748