Validation of a handheld near-infrared spectrophotometer for measurement of chemical intramuscular fat in Australian lamb.

The objective of the study was to independently validate a calibrated commercial handheld near infrared (NIR) spectroscopic device and test its repeatability over time using phenotypically diverse populations of Australian lamb. Validation testing in eight separate data sub-groups (n = 1591 carcasses overall) demonstrated that the NIR device had moderate precision (R2 = 0.4-0.64, RMSEP = 0.70-1.22%) but fluctuated in accuracy between experimental site demonstrated by variable slopes (0.50-0.94) and biases (-0.86-0.02). The repeatability experiment (n = 10 carcasses) showed that time to scan post quartering affected NIR measurement from 0 to 24 h (P < 0.001). On average, NIR IMF% was 0.97% lower (P < 0.001) at 24 h (4.01% ± 0.166), compared to 0 h. There was no difference (P > 0.05) between Time 0 and 1 h or Time 0 and 4 h or between replicate scans within each time point. This study demonstrated the SOMA NIR device could predict lamb chemical IMF% with moderate precision and accuracy, however additional work is required to understand how loin preparation, blooming and surface hydration affect NIR measurement.

BAC FISH analysis in Allium cepa.

Onion (Allium cepa L.; 1C=15,000 Mb) is an agriculturally important plant. The genome of onion has been extensively studied at the conventional cytogenetic level, but molecular analyses have lagged behind due to its large genome size. To overcome this bottleneck, a partial bacterial artificial chromosome (BAC) library of onion was constructed. The average insert size of the BAC library was about 100 kb. A total of 48,000 clones, corresponding to 0.32 genome equivalent, were obtained. Fluorescent in situ hybridization (FISH) screening resulted in identification of BAC clones localized on centromeric, telomeric, or several limited interstitial chromosomal regions, although most of the clones hybridized with entire chromosomes. The partial BAC library proved to be a useful resource for molecular cytogenetic studies of onion, and should be useful for further mapping and sequencing studies of important genes of this plant. BAC FISH screening is a powerful method for identification of molecular cytogenetic markers in large-genome plants.

Chemistry of thermal degradation of abasic sites in DNA. Mechanistic investigation on thermal DNA strand cleavage of alkylated DNA.

The chemistry of thermal degradation of aldehydic abasic sites in DNA was investigated. Sequencing gel analysis of duocarmycin A-treated 5'-32P-end-labeled DNA fragment indicated that upon heating at neutral pH alkylated DNA was cleaved to provide fragments possessing a modified sugar moiety which is readily decomposed to 3'-phosphate terminus by piperidine treatment. To identify the structure of modified sugar product and to investigate the mechanism of thermal cleavage, thermal degradation of various oligonucleotides containing abasic sites was investigated in detail. It was found that heating the DNA containing an abasic site induces beta-elimination to provide 3'-termini possessing a trans-alpha,beta-unsaturated aldose residue together with 5'-phosphate termini. Upon prolonged heating at pH 7.0, the trans-alpha,beta-unsaturated aldose terminus is isomerized to a cis isomer or is further degraded to its hydrated products and a 3'-phosphate terminus via delta-elimination. This type of thermal degradation also occurs in the abasic site-containing calf thymus DNA. Investigation of the stereochemical course of the thermal beta-elimination reaction using a 2-pro-R-D-containing abasic site has demonstrated that the reaction proceeds via a syn-elimination process as observed for the enzymatic reaction of UV endonuclease V and endonuclease III.