University of Nebraska–Lincoln

About: University of Nebraska–Lincoln is a education organization based out in Lincoln, Nebraska, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 28059 authors who have published 61544 publications receiving 2139104 citations. The organization is also known as: Nebraska & UNL.

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

Abstract: The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% of the soybean whole genome sequence developed by the Joint Genome Institute, Department of Energy, but its marker density was only sufficient to properly orient 66% of the sequence scaffolds. The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence. To that end, next generation sequencing and high-throughput genotyping were combined to obtain a much higher resolution genetic map that could be used to anchor and orient most of the remaining sequence and to help validate the integrity of the existing scaffold builds. A total of 7,108 to 25,047 predicted SNPs were discovered using a reduced representation library that was subsequently sequenced by the Illumina sequence-by-synthesis method on the clonal single molecule array platform. Using multiple SNP prediction methods, the validation rate of these SNPs ranged from 79% to 92.5%. A high resolution genetic map using 444 recombinant inbred lines was created with 1,790 SNP markers. Of the 1,790 mapped SNP markers, 1,240 markers had been selectively chosen to target existing unanchored or un-oriented sequence scaffolds, thereby increasing the amount of anchored sequence to 97%. We have demonstrated how next generation sequencing was combined with high-throughput SNP detection assays to quickly discover large numbers of SNPs. Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8× whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism.

Electric energy density of dielectric nanocomposites

Abstract: Dielectric materials with large electric energy density are actively pursued for many applications. The authors analyze the effective permittivity, breakdown strength, and electric energy density of dielectric nanocomposites using an effective medium approximation, modeling the nanocomposite as a three-phase material by the double-inclusion method. The addition of nanoparticles enhances the permittivity but reduces the breakdown strength, making the potential gain in electric energy density small. In addition, the interfacial interaction shifts the “percolation” threshold toward lower volume fraction of nanoparticles. The analysis suggests that the microstructure of nanocomposites must be carefully controlled to maintain high dielectric strength and therefore realize enhanced electric energy density.

Suggested Guidelines for Immunohistochemical Techniques in Veterinary Diagnostic Laboratories

Abstract: This document is the consensus of the American Association of Veterinary Laboratory Diagnosticians (AAVLD) Subcommittee on Standardization of Immunohistochemistry on a set of guidelines for immunohistochemistry (IHC) testing in veterinary laboratories. Immunohistochemistry is a powerful ancillary methodology frequently used in many veterinary laboratories for both diagnostic and research purposes. However, neither standardization nor validation of IHC tests has been completely achieved in veterinary medicine. This document addresses both issues. Topics covered include antibody selection, fixation, antigen retrieval, antibody incubation, antibody dilutions, tissue and reagent controls, buffers, and detection systems. The validation of an IHC test is addressed for both infectious diseases and neoplastic processes. In addition, storage and handling of IHC reagents, interpretation, quality control and assurance, and troubleshooting are also discussed. Proper standardization and validation of IHC will improve the quality of diagnostics in veterinary laboratories.

Identification of Pseudomonas syringae type III effectors that can suppress programmed cell death in plants and yeast

Abstract: Summary The Pseudomonas syringae pv. tomato DC3000 type III secretion system (TTSS) is required for bacterial pathogenicity on plants and elicitation of the hypersensitive response (HR), a programmed cell death (PCD) that occurs on resistant plants. Cosmid pHIR11 enables non-pathogens to elicit an HR dependent upon the TTSS and the effector HopPsyA. We used pHIR11 to determine that effectors HopPtoE, avirulence AvrPphEPto, AvrPpiB1Pto, AvrPtoB, and HopPtoF could suppress a HopPsyA-dependent HR on tobacco and Arabidopsis. Mixed inoculum and Agrobacterium-mediated transient expression experiments confirmed that suppressor action occurred within plant cells. These suppressors, with the exception of AvrPpiB1Pto, inhibited the expression of the tobacco pathogenesis-related (PR) gene PR1a. DC3000 suppressor mutants elicited an enhanced HR consistent with these mutants lacking an HR suppressor. Additionally, HopPtoG was identified as a suppressor on the basis of an enhanced HR produced by a hopPtoG mutant. Remarkably, these proteins functioned to inhibit the ability of the pro-apoptotic protein, Bax to induce PCD in plants and yeast, indicating that these effectors function as anti-PCD proteins in a trans-kingdom manner. The high proportion of effectors that suppress PCD suggests that suppressing plant immunity is one of the primary roles for DC3000 effectors and a central requirement for P. syringae pathogenesis.

Planning for Drought: Moving from Crisis to Risk Management

Abstract: Severe drought is a recurring problem for the United States, as illustrated by widespread economic, social, and environmental impacts Recent drought episodes and the widespread drought conditions in 1996, 1998, and 1999 emphasized this vulnerability and the need for a more proactive, risk management approach to drought management that would place greater emphasis on preparedness planning and mitigation actions Drought planning has become a principal tool of states and other levels of government to improve their response to droughts For example, since 1982, the number of states with drought plans has increased from 3 to 29 Many local governments have also adopted drought or water shortage plans Unfortunately, most state drought plans were established during the 1980s and early 1990s and emphasize emergency response or crisis management rather than risk management This paper presents a substantive revision of a 10-step drought planning process that has been applied widely in the United States and elsewhere The revised planning process places more weight on risk assessment and the development and implementation of mitigation actions and programs The goal of this paper is to encourage states to adopt this planning process in the revision of existing drought plans or, for states without plans, in the development of new plans