Oligonucleotide analysis by gel capillary electrophoresis

Several million oligonucleotides are synthesized each year for a broad variety of molecular biology applications. Steady improvements in the synthesis chemistry efficiency and the automated DNA synthesizers have made production of oligonucleotides routine and reliable. Many applications, such as PCR and sequencing, are often successful when the primers have not been rigorously purified. To ensure an adequate level of quality and purity, rapid and convenient analytical methods are necessary for the dozens of oligonucleotides produced each day by a DNA synthesis laboratory. Traditional methods of analysis have been HPLC and polyacrylamide slab tel electrophoresis (PAGE). Gel capillary electrophoresis is a new option, combining the advantages of the HPLC and PAGE, with unprecedented resolution and speed.     

Evaluating the utility of an accelerometer and urinary hormone analysis as indicators of estrus in a Zoo-housed koala (Phascolarctos cinereus)

Induced ovulators, such as the koala, do not always have overt signs of estrus, which makes pairing these animals for breeding purposes difficult to achieve in a zoo setting. This study examined the possibility of using alternative methods to behavioral sampling and weight fluctuations for monitoring estrus in a female koala of reproductive age. We attempt to gain an improved understanding of koala estrus and enhance our ability to detect it by combining a noninvasive technique for hormone analysis with a newer method for recording activity level. The findings suggest that activity levels were accurately measured using an accelerometer and increased activity was associated with one estrus behavior, bellowing. Weekly weight declines occur with increases in activity registered from the accelerometer. We also validated an assay to detect progesterone and estradiol in female koala urine in an attempt to detect an estrus spike. However, neither urinary concentrations of estradiol nor progesterone was associated with behavioral cues of estrus in our subject. We suggest that increased female activity, bellowing, and weight loss all indicate a pro-estrus state that requires proper male stimulation in order to achieve a full estrus display. Zoo Biol 28:59–68, 2009. ©2008 Wiley-Liss, Inc.     

Spatial Variation in the Bacterial and Denitrifying Bacterial Community in a Biofilter Treating Subsurface Agricultural Drainage

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples. In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria. Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect, while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics. Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically inundated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.