Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible ''euchromatin'' and ''heterochromatin.'' Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond.comparative genomics ͉ Oryza ͉ synteny T he grasses (Poaceae) provide most of mankind's caloric intake and a growing share of our fuel. The best-studied grasses, leading cereal crops, shared a common paleopolyploid ancestor Ϸ42-47 million years ago (mya) (1). Cereals show much colinearity of genetic maps and often have important traits controlled by quantitative trait loci at corresponding locations (2). Despite these similarities, the cereals have diverged remarkably in genome size from Ϸ430 million base pairs (MBP) in rice (3) to 15,966 MBP in wheat (3), largely due to differential repetitive DNA amplification and elimination.As a model for tropical grasses, sorghum [Sorghum bicolor (SB)] is a logical complement to rice (Oryza), in that it has biochemical and morphological specializations to improve carbon assimilation at high temperatures (C4 photosynthesis). By contrast, rice uses C3 photosynthesis more typical of temperate grasses. The Ϸ760-MBP (3) sorghum genome is a logical bridge to the Ϸ2,500-MBP (3) maize genome, and the Ϸ4,000-MBP (3) genome of sugarcane, the world's leading biomass͞biofuels crop. Sorghum shared common ancestry with maize (12 mya) and sugarcane (5 mya), much more recently than rice (42-47 mya). The most recent whole-genome duplication in sorghum appears to be Ϸ70 mya (1) vs. Ϸ12 mya in maize (4) and Ͻ5 mya in sugarcane (5), promising a higher success rate in relating sorghum genes to phenotypes by knockouts than either maize or sugarcane genes. Comparison of SB and closely related Sorghum...

Intact bovine ¹⁵N-α(S1)-casein was used as an internal standard in a selected reaction monitoring (SRM) assay for milk protein in baked food samples containing fats, sugar, and gums. Effects on SRM results of sample matrix composition in two biscuit recipes containing nonfat dry milk (NFDM) were studied, including samples from a milk allergen ELISA proficiency trial. Following extraction of defatted samples with carbohydrate-degrading enzymes and acid precipitation of casein, the SRM assay exhibited an LOQ of <3 ppm NFDM with 60-80% recovery. NFDM levels measured by the SRM assay were 1.7-2.5 times greater than median levels determined by ELISA. Differences were observed in the α(S1)-casein interpeptide SRM ion abundance profile between recipes and after baking. ¹⁵N-α(S1)-Casein increases SRM analysis accuracy by correcting for extraction recovery but does not eliminate underestimation of allergen concentrations due to baking-related milk protein transformation (modifications).

Unstable explosive hexamethylene triperoxide diamine (HMTD) is dangerous in quantity and benefits from the minimal sampling handling associated with atmospheric pressure chemical ionization for mass spectral analysis. Seasonal variation observed in HMTD mass spectra suggested a humidity dependence. Therefore, direct analysis in real time (DART) ionization mass spectra were acquired at a range of humidity values. An enclosure was designed to fit around the ion source and mass spectrometer inlet at atmospheric pressure. The enclosure was supplied with controlled amounts of humidified air from a test atmosphere generator to create programmable conditions for ambient analysis. The relative abundance and fragmentation of analyte ions were observed to change reliably with changing humidity values and, to a lesser degree, temperature. Humidity at such plasma-based ion sources should be regulated to avoid ∼90% shifts in relative ion abundance and provide stability and reproducibility of HMTD analysis.

Abstract. Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.