Design of a bovine low-density SNP array optimized for imputation

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.     

Development of a label-free assay for sodium-dependent phosphate transporter NaPi-IIb

The most widely used assay format for characterizing plasma membrane transporter activity measures accumulation of radiolabeled substrates in tissues or cells expressing the transporters. This assay format had limitations and disadvantages; therefore, there was an unmet need for development of a homogeneous, nonradioactive assay for membrane transporter proteins. In this report, the authors describe the development of a label-free homogeneous assay for the sodium-dependent phosphate transporter NaPi-IIb using the Epic system. The addition of phosphate stimulated a dynamic mass redistribution (DMR) profile unique to cells expressing NaPi-IIb but not on parental cells. This DMR profile was phosphate specific because sulfate or buffer alone did not elicit the same response. Furthermore, the DMR response observed was phosphate and sodium dependent, with Km values in the micromolar and millimolar range, respectively. A known NaPi-IIb noncompetitive inhibitor was shown to completely inhibit the phosphate-stimulated DMR response, suggesting that this observed DMR response is an NaPi-IIb-mediated cellular event. The results demonstrate that a novel label-free assay was developed for studying transporter-mediated cellular activity, and this DMR assay platform could be applicable to other membrane transporter proteins.     

Methods for the detection of thermotolerant campylobacters in foods: results of an inter-laboratory study

An inter-laboratory comparison of three methods for the detection of thermotolerant campylobacters is described. One of two proposed by the International Standards Organisation was significantly better for detecting campylobacters in minced chicken skin naturally contaminated at levels of either 2 or 10 cells per 10 g, but involved extensive manipulations not likely to be well received in a busy laboratory. This method yielded 18% false negative results compared with 48–54% for the other two but also gave 8% false positive results. Pre-enrichment of samples with a gradual addition of antibiotics to suppress competing organisms seemed to improve the recovery of campylobacters, as did a non-selective blood agar isolation medium used in combination with a membrane filtration technique.     

Auditory aspects of seizure in the genetically epilepsy prone rat

The organ of Corti of Genetically Epilepsy Prone Rats was examined anatomically and electrophysiologically using scanning electron microscopy (SEM) and electrophysiological recording of alternating current cochlear potentials (ACCP) and N1, a volume conductor recording of the primary auditory afferent action potentials. ACCPs for GEPRs with low intensity seizures (Acoustic Response Score (ARS) = 2 or 3) and high intensity seizures (ARS = 9) showed similar impairment in cochlear function. Approximately a 25-35 dB shift in input-output functions was present in GEPRs as compared to controls. SEM revealed several types of possible genetic abnormalities which explain the deficits in cochlear function and could serve as the basis for seizure predisposition in these animals.     

Ultrastructure of the spermatozoon of the earthworm as revealed by negative staining

This is the first demonstration of an apparent acrosome reaction by the use of negative staining (phosphotungstic acid) and electron microscopy. It is also the first report of such a reaction in spermatozoa of an oligochaete annelid (Lumbricus terrestris). The morphology of the negatively stained unreacted acrosomal complexes is entirely comparable to that seen in sectioned material. After reaction, a short straight filament is extruded and the compartmentalization seen in unreacted spermatozoa is no longer visible. In the flagellar axoneme there are short cross-bridges linking the two central singlet microtubules at 150–170 Å intervals. Two fibrous elements are also present, forming, with the singlets, a tetragon. All four of these structures apparently change their elastic properties after incubation in distilled water for two hours, so that instead of following the doublet microtubules in gentle coils, the central complex components fall as a unit in jagged configurations.     

Exploring the Potential of a School Impact on Pupil Weight Status: Exploratory Factor Analysis and Repeat Cross-Sectional Study of the National Child Measurement Programme

Schools are common sites for obesity prevention interventions. Although many theories suggest that the school context influences weight status, there has been little empirical research. The objective of this study was to explore whether features of the school context were consistently and meaningfully associated with pupil weight status (overweight or obese). Exploratory factor analysis of routinely collected data on 319 primary schools in Devon, England, was used to identify possible school-based contextual factors. Repeated cross-sectional multilevel analysis of five years (2006/07-2010/11) of data from the National Child Measurement Programme was then used to test for consistent and meaningful associations. Four school-based contextual factors were derived which ranked schools according to deprivation, location, resource and prioritisation of physical activity. None of which were meaningfully and consistently associated with pupil weight status, across the five years. The lack of consistent associations between the factors and pupil weight status suggests that the school context is not inherently obesogenic. In contrast, incorporating findings from education research indicates that schools may be equalising weight status, and obesity prevention research, policy and practice might need to address what is happening outside schools and particularly during the school holidays.     

JADE: An approach for interconnecting bioinformatics databases

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.