ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

<p>Abstract</p> <p>Background</p> <p>The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis.</p> <p>Results</p> <p>We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at <url>http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/</url>.</p> <p>Conclusions</p> <p>ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.</p

Relationship between maternal obesity and infant feeding-interactions

BACKGROUND: There are no data regarding the relationship between maternal adiposity and interaction and feeding of infants and possible contribution to childhood obesity. In this study we determined the relationship between maternal body weight and composition and infant feeding patterns and maternal-infant interaction during 24-hour metabolic rate measurements in the Enhanced Metabolic Testing Activity Chamber (EMTAC). METHODS: The amount of time four obese (BMI = 33.5 ± 5.3 kg/m(2)) and three normal weight (BMI = 23.1 ± 0.6 kg/m(2)) biological mothers, spent feeding and interacting with their infants, along with what they ingested, was recorded during 24-hour metabolic rate measurements in the EMTAC. The seven infants were 4.9 ± 0.7 months, 69 ± 3 cm, 7.5 ± 0.8 kg, 26 ± 3 % fat and 29 ± 25 percentile for weight for length. Energy and macronutrient intake (kcal/kg) were assessed. Maternal body composition was determined by air displacement plethysmorgraphy and that of the infants by skin-fold thicknesses. Pearson correlations and independent t-tests were utilized for statistical analysis (p < 0.05). RESULTS: Infants born to obese biological mothers consumed more energy (87.6 ± 18.9 vs. 68.1 ± 17.3) and energy as carbohydrate (25 ± 6 vs.16 ± 3; p < 0.05) than their normal weight counterparts. Most of the increased intake was due to complementary feedings. Twenty-four hour infant energy intake increased with both greater maternal body weight (r = 0.73;p < 0.06) and percent body fat. Furthermore, obese biological mothers spent less total time interacting (570 ± 13 vs. 381 ± 30 minutes) and feeding (298 ± 32 vs.176 ± 22 minutes) (p < 0.05) their infants than their normal weight counterparts. Twenty-four hour interaction time negatively correlated with both maternal body weight (r = -0.98; p < 0.01) and percent body fat (r = -0.92; p < 0.01). Moreover, infants of obese mothers slept more (783 ± 38 vs. 682 ± 32 minutes; p < 0.05) than their normal weight counterparts. However, there were no differences in total 24-hour energy expenditure, resting and sleeping metabolic rates (kcal/kg) for infants born to obese and normal weight biological mothers. CONCLUSION: Greater maternal body weight and percent body fat were associated with greater infant energy intakes. These infants were fed less frequently and consumed more carbohydrates in a shorter period of time as compared to infants from normal weight biological mothers. These variations in feeding patterns may predispose certain infants to obesity

Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene

Species identification techniques commonly utilized in Australian Forensic Science laboratories are gel immunodifussion antigen antibody reactions and hair comparison analysis. Both of these techniques have significant limitations and should be considered indicative opinion based tests. The Barcode of Life Initiative aims to sequence a section of DNA (~648 base pairs) for the Cytochrome Oxidase I mitochondrial gene (COI) in all living species on Earth, with the data generated being uploaded to the Barcode of Life Database (BOLD) which can then be used for species identification. The COI gene therefore offers forensics scientists an opportunity to use the marker to analyze unknown samples and compare sequences generated in BOLD. Once sequences from enough species are on the database, it is anticipated that routine identification of an unknown species may be possible. However, most forensic laboratories are not yet suited to this type of analysis and do not have the expertise to fully interpret the implications of matches and non matches involving a poorly sampled taxa (for example where there are cryptic species) and in providing the required opinion evidence. Currently, the use of BOLD is limited by the number of relevant species held in the database and the quality assurance and regulation of sequences that are there. In this paper, the COI methodology and BOLD are tested on a selection of introduced and Australian mammals in a forensic environment as the first step necessary in the implementation of this approach in the Australian context. Our data indicates that the COI methodology performs well on distinct species but needs further exploration when identifying more closely related species. It is evident from our study that changes will be required to implement DNA based wildlife forensics using the BOLD approach for forensic applications and recommendations are made for the future adoption of this technology into forensic laboratories