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

PRELIMINARY SOLUTION CRITICAL EXPERIMENTS FOR THE HIGH-FLUX ISOTOPE REACTOR

The design of the High-Flux Isotope Reactor (HFIR) was supported by a series of preliminary experiments performed at the Oak Ridge Critical Experiments Facility in 1960. The experiments yielded results describing directly some of the expected performance characteristics of the reactor and strengthened the calculational methods used in its design. The critical assembly, like the reactor, was of a flux-trap type in which a central 6-in.-dia column of H/sub 2/O was surrounded by an annulus of fissile material and, in turn, by an annular neutron reflector. The fuel region contained a solution of enriched uranyl nitrate in a mixture of H/sub 2/O and D/sub 2/O and the reflector was a composite of two annuli, the inner one of D/sub 2/O surrounded by one of H/sub 2/O. In most experiments the ends of the assembly were reflected by H/sub 2/O. Important results evaluate the absolute thermal-neutron flux to be expected in the design reactor and describe the flux distributions within this type of assembly. It was also observed that the cadmium ratio along the axis of the assembly was about 100, showing that a highly thermal-neutron flux was truly developed in the trap. It was shown that reduction of the hydrogen density in the central water column to about 80% of its normal value increased the reactivity about 6% and that further hydrogen density reduction decreased the reactivity as the effect of the loss of neutron moderation dominated the effect of the increased coupling across the central column. These considerations are of importance to the safety of the reactor. Additional experiments gave values of the usual critical dimensions and explored the effects on both the dimensions and the flux distributions of changing the concentration of the uranyl nitrate solution, of changing the composition of the solvent, and of adding neutron-absorbing materials to the D/ sub 2/O reflector. These changes were made to alter the neutron properties of the fuel solution over a range including those expected in the reactor itself. (auth

Characterization of Pseudomonas putida genes responsive to nutrient limitation

Microbiology15061661-1669MROB

Post-genomic approaches to understanding interactions between fungi and their environment

Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including sap robes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g.sap robe and opportunistic pathogen, sap robe and mycorrhizal. To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of postgenomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post- )genomic approaches to better understand fungal interactions with their environments