Polymerase chain reaction amplification of DNA from aged blood stains: quantitative evaluation of the "suitability for purpose" of four filter papers as archival media

In collaboration with the Armed Forces Institute of Pathology's Department of Defense DNA Registry, the National Institute of Standards and Technology recently evaluated the performance of a short tandem repeat multiplex with dried whole blood stains on four different commercially available identification card matrixes. DNA from 70 stains that had been stored for 19 months at ambient temperature was extracted or directly amplified and then processed using routine methods. All four storage media provided fully typeable (qualitatively identical) samples. After standardization, the average among-locus fluorescence intensity (electropherographic peak height or area) provided a suitable metric for quantitative analysis of the relative amounts of amplifiable DNA in an archived sample. The amounts of DNA in Chelex extracts from stains on two untreated high-purity cotton linter pulp papers and a paper treated with a DNA-binding coating were essentially identical. Average intensities for the aqueous extracts from a paper treated with a DNA-releasing coating were somewhat lower but also somewhat less variable than for the Chelex extracts. Average intensities of directly amplified punches of the DNA-binding paper were much larger but somewhat more variable than the Chelex extracts. Approximately 25% of the observed variation among the intensity measurements is shared among the four media and thus can be attributed to intrinsic variation in white blood count among the donors. All of the evaluated media adequately "bank" forensically useful DNA in well-dried whole blood stains for at least 19 months at ambient temperature.     

Quenched phosphorescence detection in cyclodextrin-based electrokinetic chromatography

Quenched phosphorescence detection is a sensitive detection method recently introduced in capillary zone electrophoresis. It is based on the dynamic quenching interaction of the analytes (quenchers) with a phosphorophore, 1-bromo-4-naphthalenesulfonate (BrNS), present in the separation buffer. In this study, it is shown that this detection method can also be used in cyclodextrin-based electrokinetic chromatography (CD-EKC) despite the presence in the buffer solution of cyclodextrins, which are known to reduce the luminescence quenching rate constants. Experiments indicate that BrNS mainly resides in the aqueous phase, while the analytes are distributed between both phases. In principle, the observed quenching might arise from the interaction of BrNS with uncomplexed as well as complexed analytes. However, from the dependence of the fractional quenching on the capacity factor (the normalized fractional quenching was found to be equal to the fraction of analyte in the aqueous phase), it was concluded that only aqueous-phase quenching contributes significantly to the observed quenching. Nevertheless, separation and detection can be regarded as fully compatible, because the capacity factors encountered in CD-EKC are generally low (in this study they ranged from about 0.1 to 2.5). Indeed, with nitroaromatic compounds as the target analytes, limits of detection in the 10(-8) M range were achieved.     

Speckle-contrast monitoring of tissue thermal modification

Measurements of the contrast value of time-averaged speckle-modulated images of cartilage tissue are used to study tissue thermal modification in the case of laser-light treatment. This modification is related to thermally induced internal stress relaxation in the matrix of the treated tissue. The specific feature of the evolution of time-averaged speckle contrast with a change in the current temperature of modified collagen tissue is the typical looplike form of the contrast-temperature dependencies associated with irreversible changes in tissue structure and correlated with changes in the tissue diffuse transmittance and the tissue internal stress mentioned by other researchers.     

Electrochemical oxidation of chlorophenols at a boron-doped diamond electrode and their determination by high-performance liquid chromatography with amperometric detection

Anodically pretreated diamond electrodes have been used for the detection of chlorophenols (CPs) in environmental water samples after high-performance liquid chromatographic (HPLC) separation. The anodization of as-deposited boron-doped polycrystalline diamond thin-film electrodes has enabled the stable determination of phenols over a wide concentration range. Prior to the HPLC analysis, a comparative study with ordinary glassy carbon, as-deposited diamond, and anodized diamond was made to examine the oxidative behavior of phenols by cyclic voltammety and flow injection analysis with amperometric detection. At anodized diamond electrodes, reproducible, well-defined cyclic voltammograms were obtained even at high CP concentration (5 mM), due to a low proclivity for adsorption of the oxidation products on the surface. In addition, after prolonged use, the partially deactivated diamond could be reactivated on line by applying a highly anodic potential (2.64 Vvs SCE) for 4 min, which enabled the destruction of the electrodeposited polymer deposits. Hydroxyl radicals produced by the high applied potential, in which oxygen evolution occurs, are believed to be responsible for the oxidation of the passivating layer on the surface. When coupled with flow injection analysis (FIA), anodized diamond exhibited excellent stability, with a response variability of 2.3% (n = 100), for the oxidation of a high concentration (5 mM) of chlorophenol. In contrast, glassy carbon exhibited a response variability of 39.1%. After 100 injections, the relative peak intensity, for diamond decreased by 10%, while a drastic decrease of 70% was observed for glassy carbon. The detection limit obtained in the FIA mode for 2,4-dichlorophenol was found to be 20 nM (S/N = 3), with a linear dynamic range up to 100 microM. By coupling with the column-switching technique, which enabled on-line preconcentration (50 times), the detection limit was lowered to 0.4 nM (S/N = 3). By use of this technique, anodized diamond electrodes were demonstrated for the analysis of CPs in drainwater that was condensed from the flue gas of waste incinerators.     

Insights into the cITP process using on-line NMR spectroscopy

Recently, capillary isotachophoresis (cITP) has been coupled on-line with nuclear magnetic resonance (NMR) to enhance analysis of dilute charged analytes through sample concentration and separation. This study focuses on the unique detection capabilities of NMR to noninvasively examine the cITP process and obtain diagnostic information. With their enhanced mass sensitivity, microcoil NMR probes provide optimal detection for cITP/NMR. Whereas previous studies used deuterated buffers, a 1H NMR observable leading electrolyte, tetramethylammonium acetate, is employed here to better track cITP progression. Fortuitously, the 1H chemical shift of the acetate methyl resonance depends on pD. Hence, by using a calibration curve, the solution pD can be determined on-line during cITP. Similarly, intracapillary temperature can be measured in cITP/NMR by observing the HOD chemical shift. To obtain accurate chemical shift measurements, charge-neutral tert-butyl alcohol is added to all cITP electrolyte solutions as an internal reference. As an ancillary benefit, line width measurements of the ubiquitous tert-butyl alcohol enable NMR spectral resolution to be examined throughout the experiment. Capable of providing quantitative results, NMR simultaneously determines the concentrations of the leading ion, sample, and counterion over the course of the cITP experiment.     

Tunable diode laser absorption spectroscopy in coiled hollow optical waveguides

We demonstrate tunable diode laser absorption spectroscopy of CO2 and NH3 near 1.5 microm using a distributed feedback diode laser in conjunction with hollow optical waveguides as long-path sample cells. The waveguides are coiled to reduce the physical extent of the system. The small volume of the waveguide provides rapid instrument response to changes in gas concentration. To reduce the pressure drop associated with long lengths and high flow rates, we perforate the waveguides in a novel geometry providing parallel pneumatic paths while maintaining optical path length. A minimum detectable absorbance of 3.5 x 10(-5) in a 3-m section of waveguide is demonstrated.     

The three-dimensional model of Dictyostelium discoideum racE based on the human rhoA-GDP crystal structure

The three-dimensional structure of racE was modeled using several homologous small G proteins, and the best model obtained using the human rhoA as modeling template is reported. The three-dimensional fold of the racE model is remarkably similar to the cellular form of human ras p21 crystal structure. Its secondary structure consists of six alpha-helices, six beta-strands and three 3(10) helices. The model retains its secondary structure after a 300 K, 300 ps molecular dynamics (MD) simulation. Important domains of the protein include its effector loop (residues 34-46), the insertion domain (residues 121-136), and the polybasic motif (between 210 and 220) not modeled in the current structure. The effector loop is inherently flexible and the structure docked with GDP exhibits the effector loop moving significantly closer to the nucleotide binding pocket, forming a tighter complex with the bound GDP. The mobility of the effector loop is conferred by a single residue 'hinge' point at residue 34Asp, also allowing the Switch I region, immediately preceding the effector loop, to be equally mobile. In comparison, the Switch II region shows average mobility. The insertion domain is highly flexible, with the insertion taking the form of a helical domain, with several charged residues forming a complex charged interface over the entire insertion region. While the GDP moiety is loosely held in the active site, the metal cation is extensively co-ordinated. The critical residue 38Thr exhibits high mobility, and is seen interacting directly with the metal ion at a distance of 2.64 A, and indirectly via an intervening water molecule. 64Gln, a key residue involved in GTP hydrolysis in ras, is seen facing the beta-phosphate group and the metal ion. Certain residues (i.e. 51Asn, 38Thr and 65Glu) exhibit unique characteristics and these residues, together with 158Val, may play important roles in the maintenance of the protein's integrity and function. There is strong consensus of secondary structural elements between models generated using various templates, such as h-rac1, h-rhoA and h-cdc42 bound to RhoGDI, all sharing only 50-55% sequence identity with racE, which suggests that this model is in all probability an accurate prediction of the true tertiary structure of racE.     

The role of situation assessment and flight experience in pilots' decisions to continue visual flight rules flight into adverse weather

Visual flight rules (VFR) flight into instrument meteorological conditions (IMC) is a major safety hazard in general aviation. In this study we examined pilots' decisions to continue or divert from a VFR flight into IMC during a dynamic simulation of a cross-country flight. Pilots encountered IMC either early or later into the flight, and the amount of time and distance pilots flew into the adverse weather prior to diverting was recorded. Results revealed that pilots who encountered the deteriorating weather earlier in the flight flew longer into the weather prior to diverting and had more optimistic estimates of weather conditions than did pilots who encountered the deteriorating weather later in the flight. Both the time and distance traveled into the weather prior to diverting were negatively correlated with pilots' previous flight experience. These findings suggest that VFR flight into IMC may be attributable, at least in part, to poor situation assessment and experience rather than to motivational judgment that induces risk-taking behavior as more time and effort are invested in a flight. Actual or potential applications of this research include the design of interventions that focus on improving weather evaluation skills in addition to addressing risk-taking attitudes.     

Effects of molecular oxygen on multiphoton-excited photochemical analysis of hydroxyindoles

We have examined the effects of dissolved molecular oxygen on multiphoton-excited (MPE) photochemical derivatization of serotonin (5HT) and related cellular metabolites in various buffer systems and find that oxygen has a profound effect on the formation efficiency of visible-emitting photoproducts. Previously, end-column MPE photoderivatization provided low mass detection limits for capillary electrophoretic analysis of hydroxyindoles, but relied on the use of Good's buffers to generate high-sensitivity visible signal. In the present studies, visible emission from 5HT photoderivatized in different buffers varied by 20-fold under ambient oxygen levels but less than 2-fold in the absence of oxygen; oxygen did not significantly alter the photoproduct excited-state lifetime (approximately 0.8 ns). These results support a model in which oxygen interferes with formation of visible-emitting photoproducts by quenching a reaction intermediate, an effect that can be suppressed by buffer molecules. Deoxygenation of capillary electrophoresis separation buffers improves mass detection limits for 5-hydroxyindoles fractionated in 600-nm channels by approximately 2-fold to < or =30000 molecules and provides new flexibility in identifying separation conditions for resolving 5HT from molecules with similar electrophoretic mobilities, such as the catecholamine neurotransmitters.