Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

Background: Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA) genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results: In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion: Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a resequencing microarray when their sequences differ by more than a few percent. The data suggest that interspecific cross-hybridization will not interfere with the accurate recovery of species-specific data from multispecies microarrays, provided that the species' DNA sequences differ by > 20% (mean of 5b differences per 25b oligo). Recovery of DNA sequence data from multiple, distantly-related species on a single multiplex gene chip should be a practical, highly-parallel method for investigating genomic biodiversity

Food Science and Technology Students Self-Evaluate Soft and Technical Skills

Food Scientists and Technologists (FS&T) need diverse skills in the globalized food and drink sector:Food-specific or scientific / technical skills and generic or intuitive soft skills. This study determined how satisfied FS&T students were with overall improvement, and in key technical and soft skills, based on their university work; and if satisfaction was linked to geography, degree in progress, anticipated degree, anticipated work place or anticipated job responsibility. An on-line survey was completed by 267 students in over 20 countries using a 5-point Likert scale to evaluate satisfaction. Responses were analyzed by the Friedman or Kruskal Wallis tests for more than two groups, otherwise by the Wilcoxon Signed Rank or Mann-Whitney tests. There were no differences in Overall Satisfaction with technical and soft skills training. Among soft skills, training in Working with Others and Being Responsible were more often rated “Excellent” and students were more satisfied with their training than with Solving Problems, Communication and Positive Attitude. Students anticipating a job with high responsibility were more satisfied with overall soft skill training and with 3 of the 5 specific soft skills. Among technical skills, students were more satisfied with improvement in basic sciences (Microbiology, Chemistry, Processing, Safety), and those in Northern Europe were more satisfied with overall technical training. These data show variations in perception and/or efficacy of technical and soft skill training in Food Science programmes and underline the need for separate attention to the incorporation of soft skill training into the design of FS&T course

Dark halo baryons not in ancient halo white dwarfs

Having ruled out the possibility that stellar objects are the main contributor of the dark matter embedding galaxies, microlensing experiments cannot exclude the hypothesis that a significant fraction of the Milky Way dark halo might be made of MACHOs with masses in the range 0.5-0.8 \msun. Ancient white dwarfs are generally considered the most plausible candidates for such MACHOs. We report the results of a search for such white dwarfs in a proper motion survey covering a 0.16 sqd field at three epochs at high galactic latitude, and 0.938 sqd at two epochs at intermediate galactic latitude (VIRMOS survey), using the CFH telescope. Both surveys are complete to I = 23, with detection efficiency fading to 0 at I = 24.2. Proper motion data are suitable to separate unambiguously halo white dwarfs identified by belonging to a non rotating system. No candidates were found within the colour-magnitude-proper motion volume where such objects can be safely discriminated from any standard population as well as from possible artefacts. In the same volume, we estimate the maximum white dwarf halo fraction compatible with this observation at different significance levels if the halo is at least 14 gigayears old and under different ad hoc initial mass functions. Our data alone rules out a halo fraction greater than 14% at 95% confidence level. Combined with two previous investigations exploring comparable volumes pushes the limit below 4 % (95% confidence level) or below 1.3% (64% confidence), this implies that if baryonic dark matter is present in galaxy halos, it is not, or it is only marginally in the form of faint hydrogen white dwarfs.Comment: accepted in Astronomy and Astrophysics (19-05-2004

Longitudinal impact of a youth tobacco education program

BACKGROUND: Information on the effectiveness of elementary school level, tobacco-use prevention programs is generally limited. This study assessed the impact of a structured, one-time intervention that was designed to modify attitudes and knowledge about tobacco. Participants were fifth-grade students from schools in western New York State. METHODS: Twenty-eight schools, which were in relatively close geographic proximity, were randomized into three groups; Group 1 was used to assess whether attitudes/knowledge were changed in the hypothesized direction by the intervention, and if those changes were retained four months later. Groups 2 and 3, were used as comparison groups to assess possible test-retest bias and historical effects. Groups 1 and 3 were pooled to assess whether attitudes/knowledge were changed by the intervention as measured by an immediate post-test. The non-parametric analytical techniques of Wilcoxon-Matched Pairs/Sign Ranks and the Mann-Whitney-Wilcoxon Rank Sums Tests were used to compare proportions of correct responses at each of the schools. RESULTS: Pooled analyses showed that short-term retention on most items was achieved. It was also found that retention on two knowledge items 'recognition that smokers have yellow teeth and fingers' and 'smoking one pack of cigarettes a day costs several hundred dollars per year' was maintained for four months. CONCLUSIONS: The findings suggest that inexpensive, one-time interventions for tobacco-use prevention can be of value. Changes in attitudes and knowledge conducive to the goal of tobacco-use prevention can be achieved for short-term retention and some relevant knowledge items can be retained for several months