Effect of nucleic acid binding dyes on DNA extraction,amplification, and STR typing

We report on the effects of six dyes used in the detection of DNA on the process of DNA extraction, amplification, and detection of STR loci. While dyes can be used to detect the presence of DNA, their use is restricted if they adversely affect subsequent DNA typing processes. Diamond? Nucleic Acid Dye, GelGreen?, GelRed?, RedSafe?, SYBR^® Green I, and EvaGreen? were evaluated in this study. The percentage of dye removed during the extraction process was determined to be: 70.3% for SYBR^® Green I; 99.6% for RedSafe?; 99.4% for EvaGreen?; 52.7% for Diamond? Dye; 50.6% for GelRed?, and; could not be determined for GelGreen?. It was then assumed that the amount of dye in the fluorescent quantification assay had no effect on the DNA signal. The presence of all six dyes was then reviewed for their effect on DNA extraction. The t‐test showed no significant difference between the dyes and the control. These extracts were then STR profiled and all dyes and control produced full DNA profiles. STR loci in the presence of GelGreen^TM at 1X concentration showed increased amplification products in comparison to the control samples. Full STR profiles were detected in the presence of EvaGreen? (1X), although with reduced amplification products. RedSafe? (1X), Diamond? Dye (1X), and SYBR^® Green I (1X) all exhibited varying degrees of locus drop‐out with GelRed? generating no loci at all. We provide recommendations for the best dye to visualize the presence of DNA profile as a biological stain and its subsequent amplification and detection.     

Serre''s contribution to the development of algebraic topology

We describe in detail Serre's application of spectral sequence theory to the study of the relations between the homology of total space, base space and fibre in a Serre fibration; and we apply the results to establish that a 1-connected space X has homology groups (in positive dimension) in a Serre class C if and only if its homotopy groups are in C.

We include in this paper some personal reflections on the contact the author had with Serre during the decade of the 1950's when Serre's revolutionary work in homotopy theory was completely changing the face of algebraic topology.     

HSQC-1,n-ADEQUATE: a new approach to long-range 13C-13C correlation by covariance processing

Long-range, two-dimensional heteronuclear shift correlation NMR methods play a pivotal role in the assembly of novel molecular structures. The well-established GHMBC method is a high-sensitivity mainstay technique, affording connectivity information via (n)J(CH) coupling pathways. Unfortunately, there is no simple way of determining the value of n and hence no way of differentiating two-bond from three- and occasionally four-bond correlations. Three-bond correlations, however, generally predominate. Recent work has shown that the unsymmetrical indirect covariance or generalized indirect covariance processing of multiplicity edited GHSQC and 1,1-ADEQUATE spectra provides high-sensitivity access to a (13)C-(13) C connectivity map in the form of an HSQC-1,1-ADEQUATE spectrum. Covariance processing of these data allows the 1,1-ADEQUATE connectivity information to be exploited with the inherent sensitivity of the GHSQC spectrum rather than the intrinsically lower sensitivity of the 1,1-ADEQUATE spectrum itself. Data acquisition times and/or sample size can be substantially reduced when covariance processing is to be employed. In an extension of that work, 1,n-ADEQUATE spectra can likewise be subjected to covariance processing to afford high-sensitivity access to the equivalent of (4)J(CH) GHMBC connectivity information. The method is illustrated using strychnine as a model compound.     

An adjustable linear Halbach array

The linear Halbach array is a well-known planar magnetic structure capable, in the idealized case, of generating a one-sided magnetic field. We show that such a field can be created from an array of uniformly magnetized rods, and rotating these rods in an alternating fashion can smoothly transfer the resultant magnetic field through the plane of the device. We examine an idealized model composed of infinite line dipoles and carry out computational simulations on a realizable device using a magnetic boundary element method. Such an arrangement can be used for an efficient latching device, or to produce a highly tunable field in the space above the device.     

Spatial correlation in the ambient core noise field of a turbofan engine

An acoustic transfer function relating combustion noise and turbine exit noise in the presence of enclosed ambient core noise is investigated using a dynamic system model and an acoustic system model for the particular turbofan engine studied and for a range of operating conditions. Measurements of cross-spectra magnitude and phase between the combustor and turbine exit and auto-spectra at the turbine exit and combustor are used to show the presence of indirect and direct combustion noise over the frequency range of 0-400 Hz. The procedure used evaluates the ratio of direct to indirect combustion noise. The procedure used also evaluates the post-combustion residence time in the combustor which is a factor in the formation of thermal NO(x) and soot in this region. These measurements are masked by the ambient core noise sound field in this frequency range which is observable since the transducers are situated within an acoustic wavelength of one another. An ambient core noise field model based on one and two dimensional spatial correlation functions is used to replicate the spatially correlated response of the pair of transducers. The spatial correlation function increases measured attenuation due to destructive interference and masks the true attenuation of the turbine.     

Microcalorimeter arrays for ultra-high energy resolution X- and gamma-ray detection

Microcalorimeter detectors provide superior energy resolution for the detection of X-rays and gamma-rays. The technology utilizes a cryogenic transition-edge sensor (TES) coupled to a tin bulk absorber. We are working on fabrication methods for the production of arrays with many sensors. In this paper, we present data collected with an array of microcalorimeters using as many as 26 sensor elements simultaneously. Advances in sensor design have extended the useful dynamic range to photon energies up to ～200 keV, while providing resolution performance in the 80–90 eV FWHM range, significantly better than planar high-purity germanium. These sensor arrays have applications in the measurement of nuclear materials. We present data collected from ¹⁵³Gd, a highly-enriched uranium sample, and a plutonium isotopic standard source. We also demonstrate clean separation of the ²³⁵U 185.715 keV peak from the ubiquitous ²²⁶Ra 186.211 keV background peak interference.     

Verification of a model to predict the influence of particle inertia and gravity on a decaying turbulent particle-laden flow

In an earlier publication some of the authors presented a theoretical model for the calculation of the influence of particle inertia and gravity on the turbulence in a stationary particle-laden flow. In the present publication the model is extended for application to a decaying suspension. Also a comparison is given between predictions made with the model and experimental data (own data and data reported in the literature) on a decaying turbulent flow with particles in a water tunnel or in a wind tunnel. For most of the experiments a prediction with reasonable accuracy and an interpretation is possible by means of the model.