Content and performance of the MiniMUGA genotyping array: A new tool to improve rigor and reproducibility in mouse research

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research

Kinetic emission of electrons from monocrystalline targets

This paper develops a single-collision theory of the emission of electrons from a metal surface subjected to high-energy ion bombardment, which gives reasonable agreement with the data of Carlston, Magnuson, Mahadevan, and Harrison, in the 1to 10-keV energy range. The model is based upon a Thomas-Fermi-Firsov energy-transfer calculation which has been modified to include an explicit dependence upon lattice orienta­tion. Orientation effects appear naturally, and orientation-dependent cross sections are not required, but the distribution of possible impact parameters for a particular crystal orientation is of central importance. The theory has been used to determine semiempirical interaction potentials between the moving particle and a lattice atom. These potentials are more similar to Abrahamson's atom-atom potentials than to the Gibson potentials used in radiation-damage studies.Work supported by the U.S. Office of Naval ResearchApproved for public release; distribution is unlimited

Electron ejection from single crystals due to 1- to 10-keV noble-gas ion bombardment

The secondary-electron ejection coeKcient y has been measured for the (110), (100), and (111)planes of Cu, Al, Ag, Ni, and Mo bombarded by the singly charged noble-gas ions Ne+, Ar+, Kr+, and Xe+ in the energy range from 1 to 10 keV. Surfaces were kept clean to within a fraction of a monolayer contamination by the sputtering action of the incident ion beams. The ratios ys&t/ys'q, 't' are quite constant, which would tend to indicate a theoretical model based on simple geometrical considerations of the opacity of the single crystal planes. However, the fact that the ratios are relatively insensitive to the ion-bombardment energy indicates that a model based upon the transparency of the target is not sufficient to explain the phenomenon. The dependence of y on the bombarding-ion mass is also explored

Computer circuit analysis of induced currents in the MFTF-B magnet system

An analysis was made of the induced current behavior of the MFTF-B magnet system. Although the magnet system consists of 22 coils, because of its symmetry we considered only 11 coils in the analysis. Various combinations of the coils were dumped either singly or in groups, with the current behavior in all magnets calculated as a function of time after initiation of the dump